Analysis performed on 13/01/25

Taxonomic Classification

Kraken2

Multi-Locus Sequence Typing (MLST)

Sample Organism ST 1 2 3 4 5 6 7
Sample1 klebsiella 35 gapA(2) infB(1) mdh(2) pgi(1) phoE(10) rpoB(1) tonB(19)
Sample2 klebsiella 101 gapA(2) infB(6) mdh(1) pgi(5) phoE(4) rpoB(1) tonB(6)
Sample3 saureus 45 arcC(10) aroE(14) glpF(8) gmk(6) pta(10) tpi(3) yqiL(2)
Sample4 spyogenes 28 gki(4) gtr(3) murI(4) mutS(4) recP(4) xpt(2) yqiL(4)
Sample5 ecoli_achtman_4 6057 adk(163) fumC(787) gyrB(134) icd(189) mdh(280) purA(149) recA(75)
Sample7 efaecalis 26 gdh(3) gyd(1) pstS(11) gki(12) aroE(9) xpt(14) yqiL(7)
Sample8 efaecalis 23 gdh(2) gyd(3) pstS(13) gki(11) aroE(3) xpt(2) yqiL(2)

Antimicrobial Resistance

AMRfinder plus

Sample1

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample1 aph(3’)-VI APH(3’)-VI family aminoglycoside O-phosphotransferase AMINOGLYCOSIDE AMIKACIN/KANAMYCIN 100.00 100.00 259 259 259 NODE_56_length_10210_cov_22.632192 8272 9048 \(+\) WP_014386410.1 APH(3’)-VI family aminoglycoside O-phosphotransferase NA NA NA core AMR AMR
Sample1 armA 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA AMINOGLYCOSIDE GENTAMICIN 100.00 100.00 257 257 257 NODE_60_length_7576_cov_19.451527 6517 7287 \(-\) WP_000359986.1 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA NA NA NA core AMR AMR
Sample1 arsA arsenite efflux transporter ATPase subunit ArsA ARSENIC ARSENITE 100.00 100.00 583 583 583 NODE_38_length_39957_cov_20.486008 6801 8549 \(+\) BAA24822.1 arsenite efflux transporter ATPase subunit ArsA NA NA NA plus STRESS METAL
Sample1 arsB arsenite efflux transporter membrane subunit ArsB ARSENIC ARSENITE 100.00 100.00 429 429 429 NODE_38_length_39957_cov_20.486008 8600 9886 \(+\) BAA24823.1 arsenite efflux transporter membrane subunit ArsB NA NA NA plus STRESS METAL
Sample1 arsC glutaredoxin-dependent arsenate reductase ARSENIC ARSENATE 100.00 100.00 141 141 141 NODE_38_length_39957_cov_20.486008 9902 10324 \(+\) BAA24824.1 glutaredoxin-dependent arsenate reductase NA NA NA plus STRESS METAL
Sample1 arsD arsenite efflux transporter metallochaperone ArsD ARSENIC ARSENITE 100.00 91.67 120 120 120 NODE_38_length_39957_cov_20.486008 6421 6780 \(+\) AAB09625.1 arsenite efflux transporter metallochaperone ArsD NA NA NA plus STRESS METAL
Sample1 arsR As(III)-sensing metalloregulatory transcriptional repressor ArsR ARSENIC ARSENIC 100.00 100.00 116 116 116 NODE_38_length_39957_cov_20.486008 6021 6368 \(+\) AET17094.1 As(III)-sensing metalloregulatory transcriptional repressor ArsR NA NA NA plus STRESS METAL
Sample1 blaKPC-3 carbapenem-hydrolyzing class A beta-lactamase KPC-3 BETA-LACTAM CARBAPENEM 100.00 100.00 293 293 293 NODE_45_length_23679_cov_20.948606 14049 14927 \(+\) WP_004152396.1 carbapenem-hydrolyzing class A beta-lactamase KPC-3 NA NA NA core AMR AMR
Sample1 blaNDM-1 subclass B1 metallo-beta-lactamase NDM-1 BETA-LACTAM CARBAPENEM 100.00 100.00 270 270 270 NODE_84_length_3546_cov_28.774575 2469 3278 \(-\) WP_004201164.1 subclass B1 metallo-beta-lactamase NDM-1 NA NA NA core AMR AMR
Sample1 blaOXA OXA-9 family oxacillin-hydrolyzing class D beta-lactamase BETA-LACTAM BETA-LACTAM 100.00 99.64 274 274 274 NODE_89_length_2852_cov_17.139459 244 1065 \(+\) WP_000722315.1 oxacillin-hydrolyzing class D beta-lactamase OXA-9 NA NA NA core AMR AMR
Sample1 blaSHV-1 broad-spectrum class A beta-lactamase SHV-1 BETA-LACTAM BETA-LACTAM 100.00 100.00 286 286 286 NODE_85_length_3522_cov_41.898403 23 880 \(-\) WP_001620095.1 broad-spectrum class A beta-lactamase SHV-1 NA NA NA core AMR AMR
Sample1 blaTEM-1 broad-spectrum class A beta-lactamase TEM-1 BETA-LACTAM BETA-LACTAM 100.00 100.00 286 286 286 NODE_89_length_2852_cov_17.139459 1768 2625 \(+\) WP_000027057.1 broad-spectrum class A beta-lactamase TEM-1 NA NA NA core AMR AMR
Sample1 ble bleomycin binding protein Ble-MBL BLEOMYCIN BLEOMYCIN 100.00 100.00 121 121 121 NODE_84_length_3546_cov_28.774575 2100 2462 \(-\) WP_004201167.1 bleomycin binding protein Ble-MBL NA NA NA core AMR AMR
Sample1 clpK heat shock survival AAA family ATPase ClpK NA NA 97.89 99.25 929 949 929 NODE_65_length_6396_cov_25.027694 2380 5166 \(-\) ASF80763.1 heat shock survival AAA family ATPase ClpK NA NA NA plus STRESS HEAT
Sample1 crcB fluoride efflux transporter CrcB FLUORIDE FLUORIDE 100.00 100.00 137 137 137 NODE_26_length_87806_cov_31.164963 37032 37442 \(+\) CCN31428.1 fluoride efflux transporter CrcB NA NA NA plus STRESS BIOCIDE
Sample1 dfrA5 trimethoprim-resistant dihydrofolate reductase DfrA5 TRIMETHOPRIM TRIMETHOPRIM 100.00 100.00 157 157 157 NODE_82_length_3659_cov_26.867113 1429 1899 \(+\) WP_001317507.1 trimethoprim-resistant dihydrofolate reductase DfrA5 NA NA NA core AMR AMR
Sample1 emrD multidrug efflux MFS transporter EmrD EFFLUX EFFLUX 100.00 99.49 394 394 394 NODE_23_length_100834_cov_38.618567 79981 81162 \(-\) ACN65732.1 multidrug efflux MFS transporter EmrD NA NA NA plus AMR AMR
Sample1 fieF CDF family cation-efflux transporter FieF NA NA 100.00 100.00 300 300 300 NODE_24_length_99615_cov_37.725321 58945 59844 \(+\) BAB89353.1 CDF family cation-efflux transporter FieF NA NA NA plus STRESS METAL
Sample1 fosA FosA5 family fosfomycin resistance glutathione transferase FOSFOMYCIN FOSFOMYCIN 100.00 100.00 139 139 139 NODE_14_length_151513_cov_31.882346 135675 136091 \(-\) WP_004146118.1 FosA5 family fosfomycin resistance glutathione transferase NA NA NA core AMR AMR
Sample1 hsp20 small heat shock protein sHSP20 NA NA 100.00 100.00 189 189 189 NODE_65_length_6396_cov_25.027694 5284 5850 \(-\) CDY80020.1 small heat shock protein sHSP20 NA NA NA plus STRESS HEAT
Sample1 iucA aerobactin synthase IucA NA NA 99.83 90.09 573 576 575 NODE_42_length_31563_cov_23.613003 5218 6936 \(+\) EGI25746.1 aerobactin synthase IucA NA NA NA plus VIRULENCE VIRULENCE
Sample1 iucB N(6)-hydroxylysine O-acetyltransferase IucB NA NA 100.00 94.60 315 315 315 NODE_42_length_31563_cov_23.613003 6943 7887 \(+\) AAN82074.1 N(6)-hydroxylysine O-acetyltransferase IucB NA NA NA plus VIRULENCE VIRULENCE
Sample1 iucC NIS family aerobactin synthetase IucC NA NA 99.48 92.72 577 580 577 NODE_42_length_31563_cov_23.613003 7890 9620 \(+\) AAN82073.1 NIS family aerobactin synthetase IucC NA NA NA plus VIRULENCE VIRULENCE
Sample1 kdeA multidrug efflux MFS transporter KdeA EFFLUX EFFLUX 100.00 100.00 410 410 410 NODE_13_length_161606_cov_24.101585 99195 100424 \(+\) ABR76310.1 multidrug efflux MFS transporter KdeA NA NA NA plus AMR AMR
Sample1 mchF microcin H47 export transporter peptidase/ATP-binding subunit MchF NA NA 100.00 100.00 698 698 698 NODE_2_length_385203_cov_24.836368 355682 357775 \(+\) AAL08400.1 microcin H47 export transporter peptidase/ATP-binding subunit MchF NA NA NA plus VIRULENCE VIRULENCE
Sample1 merC organomercurial transporter MerC MERCURY ORGANOMERCURY 100.00 100.00 140 140 140 NODE_71_length_5110_cov_22.533876 223 642 \(+\) AAC33908.1 organomercurial transporter MerC NA NA NA plus STRESS METAL
Sample1 mph(A) Mph(A) family macrolide 2’-phosphotransferase MACROLIDE AZITHROMYCIN/ERYTHROMYCIN/SPIRAMYCIN/TELITHROMYCIN 100.00 100.00 301 301 301 NODE_68_length_6118_cov_26.757987 147 1049 \(+\) WP_000219391.1 Mph(A) family macrolide 2’-phosphotransferase NA NA NA core AMR AMR
Sample1 mph(E) Mph(E) family macrolide 2’-phosphotransferase MACROLIDE ERYTHROMYCIN 100.00 100.00 294 294 294 NODE_60_length_7576_cov_19.451527 1803 2684 \(-\) WP_000155092.1 Mph(E) family macrolide 2’-phosphotransferase NA NA NA core AMR AMR
Sample1 msr(E) ABC-F type ribosomal protection protein Msr(E) MACROLIDE/STREPTOGRAMIN AZITHROMYCIN/ERYTHROMYCIN/STREPTOGRAMIN 100.00 100.00 491 491 491 NODE_60_length_7576_cov_19.451527 2743 4215 \(-\) WP_000052512.1 ABC-F type ribosomal protection protein Msr(E) NA NA NA core AMR AMR
Sample1 oqxA4 multidrug efflux RND transporter periplasmic adaptor subunit OqxA4 PHENICOL/QUINOLONE PHENICOL/QUINOLONE 100.00 100.00 391 391 391 NODE_17_length_122842_cov_28.181868 64068 65240 \(+\) WP_063865368.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA4 NA NA NA core AMR AMR
Sample1 oqxB19 multidrug efflux RND transporter permease subunit OqxB19 PHENICOL/QUINOLONE PHENICOL/QUINOLONE 100.00 100.00 1050 1050 1050 NODE_17_length_122842_cov_28.181868 65267 68416 \(+\) WP_004149399.1 multidrug efflux RND transporter permease subunit OqxB19 NA NA NA core AMR AMR
Sample1 pcoA multicopper oxidase PcoA COPPER COPPER 100.00 100.00 605 605 605 NODE_38_length_39957_cov_20.486008 23399 25213 \(-\) CAA58525.1 multicopper oxidase PcoA NA NA NA plus STRESS METAL
Sample1 pcoB copper-binding protein PcoB COPPER COPPER 100.00 100.00 296 296 296 NODE_38_length_39957_cov_20.486008 22503 23390 \(-\) CAA58526.1 copper-binding protein PcoB NA NA NA plus STRESS METAL
Sample1 pcoC copper resistance system metallochaperone PcoC COPPER COPPER 100.00 100.00 126 126 126 NODE_38_length_39957_cov_20.486008 22083 22460 \(-\) CAA58527.1 copper resistance system metallochaperone PcoC NA NA NA plus STRESS METAL
Sample1 pcoD copper resistance inner membrane protein PcoD COPPER COPPER 100.00 99.68 309 309 309 NODE_38_length_39957_cov_20.486008 21149 22075 \(-\) CAA58528.1 copper resistance inner membrane protein PcoD NA NA NA plus STRESS METAL
Sample1 pcoE copper resistance system metallochaperone PcoE COPPER COPPER 100.00 94.44 144 144 144 NODE_38_length_39957_cov_20.486008 18366 18797 \(-\) CAA58532.1 copper resistance system metallochaperone PcoE NA NA NA plus STRESS METAL
Sample1 pcoR copper response regulator transcription factor PcoR COPPER COPPER 100.00 100.00 226 226 226 NODE_38_length_39957_cov_20.486008 20414 21091 \(-\) CAA58529.1 copper response regulator transcription factor PcoR NA NA NA plus STRESS METAL
Sample1 pcoS copper resistance membrane spanning protein PcoS COPPER COPPER 100.00 99.14 466 466 466 NODE_38_length_39957_cov_20.486008 19017 20414 \(-\) CAA58530.1 copper resistance membrane spanning protein PcoS NA NA NA plus STRESS METAL
Sample1 qacEdelta1 quaternary ammonium compound efflux SMR transporter QacE delta 1 QUATERNARY AMMONIUM QUATERNARY AMMONIUM 100.00 100.00 115 115 115 NODE_82_length_3659_cov_26.867113 2086 2430 \(+\) WP_000679427.1 quaternary ammonium compound efflux SMR transporter QacE delta 1 NA NA NA core STRESS BIOCIDE
Sample1 qnrS1 quinolone resistance pentapeptide repeat protein QnrS1 QUINOLONE QUINOLONE 100.00 100.00 218 218 218 NODE_56_length_10210_cov_22.632192 3738 4391 \(+\) WP_001516695.1 quinolone resistance pentapeptide repeat protein QnrS1 NA NA NA core AMR AMR
Sample1 silA Cu(+)/Ag(+) efflux RND transporter permease subunit SilA COPPER/SILVER COPPER/SILVER 100.00 98.85 1048 1048 1048 NODE_38_length_39957_cov_20.486008 30298 33441 \(-\) AAD11749.1 Cu(+)/Ag(+) efflux RND transporter permease subunit SilA NA NA NA plus STRESS METAL
Sample1 silB Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB COPPER/SILVER COPPER/SILVER 100.00 97.67 430 430 430 NODE_38_length_39957_cov_20.486008 33455 34744 \(-\) AAD11748.1 Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB NA NA NA plus STRESS METAL
Sample1 silC Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC COPPER/SILVER COPPER/SILVER 100.00 100.00 461 461 461 NODE_38_length_39957_cov_20.486008 35243 36625 \(-\) SPD96884.1 Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC NA NA NA plus STRESS METAL
Sample1 silE silver-binding protein SilE SILVER SILVER 100.00 91.61 143 143 143 NODE_38_length_39957_cov_20.486008 39214 39642 \(+\) AAD11743.1 silver-binding protein SilE NA NA NA plus STRESS METAL
Sample1 silF Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone SilF COPPER/SILVER COPPER/SILVER 100.00 99.15 117 117 117 NODE_38_length_39957_cov_20.486008 34861 35211 \(-\) KGL71342.1 Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone SilF NA NA NA plus STRESS METAL
Sample1 silP Ag(+)-translocating P-type ATPase SilP SILVER SILVER 99.64 94.53 822 824 823 NODE_38_length_39957_cov_20.486008 27197 29662 \(-\) AAD11750.1 Ag(+)-translocating P-type ATPase SilP NA NA NA plus STRESS METAL
Sample1 silR copper/silver response regulator transcription factor SilR COPPER/SILVER COPPER/SILVER 100.00 100.00 226 226 226 NODE_38_length_39957_cov_20.486008 36815 37492 \(+\) SPD96883.1 copper/silver response regulator transcription factor SilR NA NA NA plus STRESS METAL
Sample1 silS copper/silver sensor histidine kinase SilS COPPER/SILVER COPPER/SILVER 100.00 100.00 491 491 491 NODE_38_length_39957_cov_20.486008 37488 38960 \(+\) SPD96882.1 copper/silver sensor histidine kinase SilS NA NA NA plus STRESS METAL
Sample1 sul1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE SULFONAMIDE 100.00 100.00 279 279 279 NODE_82_length_3659_cov_26.867113 2427 3263 \(+\) WP_000259031.1 sulfonamide-resistant dihydropteroate synthase Sul1 NA NA NA core AMR AMR
Sample1 sul2 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE SULFONAMIDE 100.00 100.00 271 271 271 NODE_67_length_6209_cov_27.717221 3886 4698 \(-\) WP_001043260.1 sulfonamide-resistant dihydropteroate synthase Sul2 NA NA NA core AMR AMR
Sample1 ybtP yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA 100.00 99.83 600 600 600 NODE_1_length_409520_cov_22.884123 52026 53825 \(+\) CAA21388.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA NA plus VIRULENCE VIRULENCE
Sample1 ybtQ yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA 100.00 99.83 600 600 600 NODE_1_length_409520_cov_22.884123 53815 55614 \(+\) AAC69584.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA NA plus VIRULENCE VIRULENCE


Sample2

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample2 aadA1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 AMINOGLYCOSIDE STREPTOMYCIN 100.00 100.00 262 262 262 NODE_59_length_8503_cov_27.463684 1271 2056 \(+\) WP_001206315.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 NA NA NA core AMR AMR
Sample2 ant(2’’)-Ia aminoglycoside nucleotidyltransferase ANT(2’’)-Ia AMINOGLYCOSIDE GENTAMICIN/KANAMYCIN/TOBRAMYCIN 100.00 100.00 177 177 177 NODE_59_length_8503_cov_27.463684 680 1210 \(+\) WP_000381802.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia NA NA NA core AMR AMR
Sample2 armA 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA AMINOGLYCOSIDE GENTAMICIN 100.00 100.00 257 257 257 NODE_66_length_5980_cov_31.768592 273 1043 \(+\) WP_000359986.1 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA NA NA NA core AMR AMR
Sample2 blaKPC-3 carbapenem-hydrolyzing class A beta-lactamase KPC-3 BETA-LACTAM CARBAPENEM 100.00 100.00 293 293 293 NODE_48_length_21954_cov_52.979888 17158 18036 \(+\) WP_004152396.1 carbapenem-hydrolyzing class A beta-lactamase KPC-3 NA NA NA core AMR AMR
Sample2 blaSHV-1 broad-spectrum class A beta-lactamase SHV-1 BETA-LACTAM BETA-LACTAM 100.00 100.00 286 286 286 NODE_13_length_143880_cov_22.251622 115086 115943 \(+\) WP_001620095.1 broad-spectrum class A beta-lactamase SHV-1 NA NA NA core AMR AMR
Sample2 catA1 type A-1 chloramphenicol O-acetyltransferase PHENICOL CHLORAMPHENICOL 100.00 100.00 219 219 219 NODE_87_length_1659_cov_21.879267 300 956 \(+\) WP_000412211.1 type A-1 chloramphenicol O-acetyltransferase NA NA NA core AMR AMR
Sample2 emrD multidrug efflux MFS transporter EmrD EFFLUX EFFLUX 100.00 99.49 394 394 394 NODE_19_length_100488_cov_34.283584 19316 20497 \(+\) ACN65732.1 multidrug efflux MFS transporter EmrD NA NA NA plus AMR AMR
Sample2 fieF CDF family cation-efflux transporter FieF NA NA 100.00 100.00 300 300 300 NODE_20_length_99576_cov_33.391240 39775 40674 \(-\) BAB89353.1 CDF family cation-efflux transporter FieF NA NA NA plus STRESS METAL
Sample2 fosA FosA5 family fosfomycin resistance glutathione transferase FOSFOMYCIN FOSFOMYCIN 100.00 98.56 139 139 139 NODE_25_length_81436_cov_30.505341 66699 67115 \(-\) WP_114473955.1 fosfomycin resistance glutathione transferase FosA9 NA NA NA core AMR AMR
Sample2 iucB N(6)-hydroxylysine O-acetyltransferase IucB NA NA 100.00 94.60 315 315 315 NODE_51_length_18440_cov_24.502042 6943 7887 \(+\) AAN82074.1 N(6)-hydroxylysine O-acetyltransferase IucB NA NA NA plus VIRULENCE VIRULENCE
Sample2 iucC NIS family aerobactin synthetase IucC NA NA 99.48 92.72 577 580 577 NODE_51_length_18440_cov_24.502042 7890 9620 \(+\) AAN82073.1 NIS family aerobactin synthetase IucC NA NA NA plus VIRULENCE VIRULENCE
Sample2 kdeA multidrug efflux MFS transporter KdeA EFFLUX EFFLUX 100.00 99.76 410 410 410 NODE_26_length_79693_cov_24.311143 71256 72485 \(+\) ABR76310.1 multidrug efflux MFS transporter KdeA NA NA NA plus AMR AMR
Sample2 merA mercury(II) reductase MERCURY MERCURY 100.00 93.23 561 561 561 NODE_62_length_7283_cov_54.485845 4849 6531 \(+\) ACU65296.1 mercury(II) reductase NA NA NA plus STRESS METAL
Sample2 merD mercury resistance co-regulator MerD MERCURY MERCURY 100.00 90.08 121 121 121 NODE_62_length_7283_cov_54.485845 6552 6914 \(+\) AAC38221.1 mercury resistance co-regulator MerD NA NA NA plus STRESS METAL
Sample2 merE broad-spectrum mercury transporter MerE MERCURY MERCURY 100.00 96.15 78 78 78 NODE_62_length_7283_cov_54.485845 6914 7147 \(+\) AAC38236.1 broad-spectrum mercury transporter MerE NA NA NA plus STRESS METAL
Sample2 merR mercury resistance transcriptional regulator MerR MERCURY MERCURY 98.61 92.96 142 144 142 NODE_62_length_7283_cov_54.485845 3204 3629 \(-\) CAA77320.1 mercury resistance transcriptional regulator MerR NA NA NA plus STRESS METAL
Sample2 merT mercuric transport protein MerT MERCURY MERCURY 99.14 98.26 115 116 115 NODE_62_length_7283_cov_54.485845 3719 4063 \(+\) CAA70196.1 mercuric transport protein MerT NA NA NA plus STRESS METAL
Sample2 mph(E) Mph(E) family macrolide 2’-phosphotransferase MACROLIDE ERYTHROMYCIN 100.00 100.00 294 294 294 NODE_66_length_5980_cov_31.768592 4876 5757 \(+\) WP_000155092.1 Mph(E) family macrolide 2’-phosphotransferase NA NA NA core AMR AMR
Sample2 msr(E) ABC-F type ribosomal protection protein Msr(E) MACROLIDE/STREPTOGRAMIN AZITHROMYCIN/ERYTHROMYCIN/STREPTOGRAMIN 100.00 100.00 491 491 491 NODE_66_length_5980_cov_31.768592 3345 4817 \(+\) WP_000052512.1 ABC-F type ribosomal protection protein Msr(E) NA NA NA core AMR AMR
Sample2 oqxA multidrug efflux RND transporter periplasmic adaptor subunit OqxA PHENICOL/QUINOLONE PHENICOL/QUINOLONE 100.00 100.00 391 391 391 NODE_24_length_84154_cov_26.506904 53669 54841 \(-\) WP_002914189.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA NA NA NA core AMR AMR
Sample2 oqxB20 multidrug efflux RND transporter permease subunit OqxB20 PHENICOL/QUINOLONE PHENICOL/QUINOLONE 100.00 100.00 1050 1050 1050 NODE_24_length_84154_cov_26.506904 50493 53642 \(-\) WP_021312368.1 multidrug efflux RND transporter permease subunit OqxB20 NA NA NA core AMR AMR
Sample2 qacEdelta1 quaternary ammonium compound efflux SMR transporter QacE delta 1 QUATERNARY AMMONIUM QUATERNARY AMMONIUM 100.00 100.00 115 115 115 NODE_59_length_8503_cov_27.463684 2223 2567 \(+\) WP_000679427.1 quaternary ammonium compound efflux SMR transporter QacE delta 1 NA NA NA core STRESS BIOCIDE
Sample2 sul1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE SULFONAMIDE 100.00 100.00 279 279 279 NODE_59_length_8503_cov_27.463684 2564 3400 \(+\) WP_000259031.1 sulfonamide-resistant dihydropteroate synthase Sul1 NA NA NA core AMR AMR
Sample2 terB tellurium resistance membrane protein TerB TELLURIUM TELLURIUM 100.00 99.34 151 151 151 NODE_33_length_50445_cov_22.742555 25241 25693 \(-\) ACI12150.1 tellurium resistance membrane protein TerB NA NA NA plus STRESS METAL
Sample2 terC tellurium resistance membrane protein TerC TELLURIUM TELLURIUM 100.00 99.13 346 346 346 NODE_33_length_50445_cov_22.742555 24177 25214 \(-\) AAA98291.1 tellurium resistance membrane protein TerC NA NA NA plus STRESS METAL
Sample2 terD tellurium resistance membrane protein TerD TELLURIUM TELLURIUM 100.00 98.96 192 192 192 NODE_33_length_50445_cov_22.742555 23560 24135 \(-\) AAA98292.1 tellurium resistance membrane protein TerD NA NA NA plus STRESS METAL
Sample2 terE tellurium resistance cAMP binding protein TerE TELLURIUM TELLURIUM 100.00 99.48 191 191 191 NODE_33_length_50445_cov_22.742555 22898 23470 \(-\) AAA98293.1 tellurium resistance cAMP binding protein TerE NA NA NA plus STRESS METAL
Sample2 ybtP yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA 100.00 99.83 600 600 600 NODE_18_length_118566_cov_22.645967 90919 92718 \(+\) CAA21388.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtP NA NA NA plus VIRULENCE VIRULENCE
Sample2 ybtQ yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA 100.00 99.83 600 600 600 NODE_18_length_118566_cov_22.645967 92708 94507 \(+\) AAC69584.1 yersiniabactin ABC transporter ATP-binding/permease protein YbtQ NA NA NA plus VIRULENCE VIRULENCE


Sample3

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample3 aur zinc metalloproteinase aureolysin NA NA 100.00 93.52 509 509 509 NODE_18_length_42988_cov_83.614353 32482 34008 \(+\) EHO93748.1 zinc metalloproteinase aureolysin NA NA NA plus VIRULENCE VIRULENCE
Sample3 blaI penicillinase repressor BlaI BETA-LACTAM BETA-LACTAM 96.03 99.17 121 126 121 NODE_89_length_3290_cov_522.302009 2 364 \(-\) WP_001284656.1 penicillinase repressor BlaI NA NA NA core AMR AMR
Sample3 blaR1 beta-lactam sensor/signal transducer BlaR1 BETA-LACTAM BETA-LACTAM 100.00 95.56 585 585 585 NODE_89_length_3290_cov_522.302009 357 2111 \(-\) WP_001096386.1 beta-lactam sensor/signal transducer BlaR1 NA NA NA core AMR AMR
Sample3 blaZ penicillin-hydrolyzing class A beta-lactamase BlaZ BETA-LACTAM BETA-LACTAM 100.00 100.00 281 281 281 NODE_89_length_3290_cov_522.302009 2218 3060 \(+\) WP_000733289.1 penicillin-hydrolyzing class A beta-lactamase BlaZ NA NA NA core AMR AMR
Sample3 cadD cadmium resistance transporter CadD CADMIUM CADMIUM 100.00 99.51 205 205 205 NODE_95_length_2412_cov_526.154858 1122 1736 \(+\) BAB43874.1 cadmium resistance transporter CadD NA NA NA plus STRESS METAL
Sample3 glpT_A100V Staphylococcus aureus fosfomycin resistant GlpT FOSFOMYCIN FOSFOMYCIN 100.00 99.78 452 452 452 NODE_7_length_75822_cov_72.897277 35733 37088 \(-\) WP_001010111.1 glycerol-3-phosphate transporter GlpT NA NA NA core AMR POINT
Sample3 hld delta-hemolysin NA NA 100.00 100.00 26 26 26 NODE_8_length_72322_cov_70.965074 32308 32385 \(+\) AGU62139.1 delta-hemolysin NA NA NA plus VIRULENCE VIRULENCE
Sample3 hlgA bi-component gamma-hemolysin HlgAB subunit A NA NA 100.00 99.68 309 309 309 NODE_6_length_102568_cov_74.986460 65305 66231 \(-\) AUU54669.1 bi-component gamma-hemolysin HlgAB subunit A NA NA NA plus VIRULENCE VIRULENCE
Sample3 hlgB bi-component gamma-hemolysin HlgAB/HlgCB subunit B NA NA 100.00 99.38 325 325 325 NODE_6_length_102568_cov_74.986460 62811 63785 \(-\) CAA57278.1 bi-component gamma-hemolysin HlgAB/HlgCB subunit B NA NA NA plus VIRULENCE VIRULENCE
Sample3 hlgC bi-component gamma-hemolysin HlgCB subunit C NA NA 100.00 97.14 315 315 315 NODE_6_length_102568_cov_74.986460 63790 64734 \(-\) CAA57277.1 bi-component gamma-hemolysin HlgCB subunit C NA NA NA plus VIRULENCE VIRULENCE
Sample3 icaC polysaccharide intercellular adhesin biosynthesis/export protein IcaC NA NA 100.00 99.71 350 350 350 NODE_56_length_12340_cov_94.944078 245 1294 \(-\) AUU58561.1 polysaccharide intercellular adhesin biosynthesis/export protein IcaC NA NA NA plus VIRULENCE VIRULENCE
Sample3 lmrS multidrug efflux MFS transporter LmrS MACROLIDE/PHENICOL CHLORAMPHENICOL/ERYTHROMYCIN 100.00 96.25 480 480 480 NODE_69_length_8519_cov_70.341210 1651 3090 \(-\) AAW38464.1 multidrug efflux MFS transporter LmrS NA NA NA plus STRESS BIOCIDE
Sample3 mepA multidrug efflux MATE transporter MepA TETRACYCLINE TIGECYCLINE 100.00 99.11 451 451 451 NODE_7_length_75822_cov_72.897277 33749 35101 \(+\) BAB41547.1 multidrug efflux MATE transporter MepA NA NA NA plus AMR AMR
Sample3 murA_E291D Staphylococcus aureus fosfomycin resistant MurA FOSFOMYCIN FOSFOMYCIN 100.00 99.52 421 421 421 NODE_23_length_36704_cov_63.869410 34857 36119 \(+\) WP_000358006.1 UDP-N-acetylglucosamine 1-carboxyvinyltransferase MurA NA NA NA core AMR POINT
Sample3 murA_T396N Staphylococcus aureus fosfomycin resistant MurA FOSFOMYCIN FOSFOMYCIN 100.00 99.52 421 421 421 NODE_23_length_36704_cov_63.869410 34857 36119 \(+\) WP_000358006.1 UDP-N-acetylglucosamine 1-carboxyvinyltransferase MurA NA NA NA core AMR POINT
Sample3 sak staphylokinase NA NA 100.00 98.77 163 163 163 NODE_48_length_18462_cov_162.282990 16961 17449 \(+\) CAA24957.1 staphylokinase NA NA NA plus VIRULENCE VIRULENCE
Sample3 scn complement inhibitor SCIN-A NA NA 100.00 100.00 116 116 116 NODE_98_length_2325_cov_187.610573 772 1119 \(+\) ADL23798.1 complement inhibitor SCIN-A NA NA NA plus VIRULENCE VIRULENCE
Sample3 sec2 staphylococcal enterotoxin type C2 NA NA 100.00 100.00 266 266 266 NODE_32_length_30161_cov_64.399488 5180 5977 \(+\) AAA26624.1 staphylococcal enterotoxin type C2 NA NA NA plus VIRULENCE VIRULENCE
Sample3 sei staphylococcal enterotoxin type I NA NA 99.59 93.39 242 243 242 NODE_60_length_10708_cov_61.516662 4629 5354 \(-\) SGR88193.1 staphylococcal enterotoxin type I NA NA NA plus VIRULENCE VIRULENCE
Sample3 sel staphylococcal enterotoxin type L NA NA 100.00 98.75 240 240 240 NODE_32_length_30161_cov_64.399488 6150 6869 \(-\) AMG40538.1 staphylococcal enterotoxin type L NA NA NA plus VIRULENCE VIRULENCE
Sample3 sel26 staphylococcal enterotoxin type 26 NA NA 100.00 96.40 250 250 250 NODE_2_length_257385_cov_46.985552 71828 72577 \(+\) KAG18833.1 staphylococcal enterotoxin type 26 NA NA NA plus VIRULENCE VIRULENCE
Sample3 sem staphylococcal enterotoxin type M NA NA 100.00 93.72 239 239 239 NODE_60_length_10708_cov_61.516662 5392 6108 \(-\) SGR88215.1 staphylococcal enterotoxin type M NA NA NA plus VIRULENCE VIRULENCE
Sample3 sen staphylococcal enterotoxin type N NA NA 100.00 99.63 272 272 272 NODE_60_length_10708_cov_61.516662 2848 3663 \(-\) SAO78304.1 staphylococcal enterotoxin type N NA NA NA plus VIRULENCE VIRULENCE
Sample3 seo staphylococcal enterotoxin type O NA NA 100.00 100.00 260 260 260 NODE_60_length_10708_cov_61.516662 6391 7170 \(-\) BAB42916.1 staphylococcal enterotoxin type O NA NA NA plus VIRULENCE VIRULENCE
Sample3 seu staphylococcal enterotoxin type U NA NA 100.00 94.25 256 261 261 NODE_60_length_10708_cov_61.516662 3705 4472 \(-\) SGR88168.1 staphylococcal enterotoxin type U NA NA NA plus VIRULENCE VIRULENCE
Sample3 tet(38) tetracycline efflux MFS transporter Tet(38) TETRACYCLINE TETRACYCLINE 100.00 100.00 450 450 450 NODE_87_length_3816_cov_82.890189 574 1923 \(-\) WP_001100293.1 tetracycline efflux MFS transporter Tet(38) NA NA NA core AMR AMR


Sample5

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample5 acrF multidrug efflux RND transporter permease subunit AcrF EFFLUX EFFLUX 100 96.23 1034 1034 1034 NODE_2_length_652771_cov_13.1584 1719 4820 \(-\) AAC76298.1 multidrug efflux RND transporter permease subunit AcrF NA NA NA plus AMR AMR
Sample5 cdtB cytolethal distending toxin type II nuclease subunit CdtB NA NA 100 100.00 269 269 269 NODE_4_length_290048_cov_13.1184 54863 55669 \(+\) BAH72965.1 cytolethal distending toxin type II nuclease subunit CdtB NA NA NA plus VIRULENCE VIRULENCE
Sample5 eae intimin type gamma INTIMIN GAMMA 100 99.14 935 935 935 NODE_9_length_234966_cov_12.9153 43943 46747 \(+\) ACM67164.1 intimin type gamma NA NA NA plus VIRULENCE VIRULENCE
Sample5 emrD multidrug efflux MFS transporter EmrD EFFLUX EFFLUX 100 97.73 396 396 396 NODE_7_length_258688_cov_13.1509 70631 71818 \(-\) EFF04178.1 multidrug efflux MFS transporter EmrD NA NA NA plus AMR AMR
Sample5 emrE multidrug efflux SMR transporter EmrE EFFLUX EFFLUX 100 96.36 110 110 110 NODE_5_length_284821_cov_12.9843 104152 104481 \(-\) CAA77936.1 multidrug efflux SMR transporter EmrE NA NA NA plus STRESS BIOCIDE
Sample5 espA type III secretion system LEE translocon filament protein EspA NA NA 100 96.35 192 192 192 NODE_9_length_234966_cov_12.9153 49522 50097 \(+\) CAI43862.1 type III secretion system LEE translocon filament protein EspA NA NA NA plus VIRULENCE VIRULENCE
Sample5 espB type III secretion system LEE translocon pore-forming subunit EspB NA NA 100 100.00 314 314 314 NODE_9_length_234966_cov_12.9153 51276 52217 \(+\) AAC82360.1 type III secretion system LEE translocon pore-forming subunit EspB NA NA NA plus VIRULENCE VIRULENCE
Sample5 glpT_E448K Escherichia fosfomycin resistant GlpT FOSFOMYCIN FOSFOMYCIN 100 97.57 452 452 452 NODE_4_length_290048_cov_13.1184 252370 253725 \(-\) WP_000948731.1 glycerol-3-phosphate transporter GlpT NA NA NA core AMR POINT
Sample5 ibeA putative intracellular survival FAD-dependent oxidoreductase IbeA NA NA 100 92.76 456 456 456 NODE_16_length_116703_cov_13.7971 32121 33488 \(+\) AAF98391.2 putative intracellular survival FAD-dependent oxidoreductase IbeA NA NA NA plus VIRULENCE VIRULENCE
Sample5 iss increased serum survival lipoprotein Iss NA NA 100 97.94 97 97 97 NODE_5_length_284821_cov_12.9843 246803 247093 \(+\) ADR26561.1 increased serum survival lipoprotein Iss NA NA NA plus VIRULENCE VIRULENCE
Sample5 marR_S3N Escherichia ampicillin/chloramphenicol/quinolone/rifampin/tetracycline resistant MarR MULTIDRUG AMPICILLIN/CHLORAMPHENICOL/QUINOLONE/RIFAMPIN/TETRACYCLINE 100 94.44 144 144 144 NODE_10_length_224891_cov_13.1742 22842 23273 \(+\) WP_000843414.1 transcriptional regulator MarR NA NA NA core AMR POINT
Sample5 parE_I355T Escherichia quinolone resistant ParE QUINOLONE QUINOLONE 100 98.41 630 630 630 NODE_2_length_652771_cov_13.1584 237322 239211 \(+\) WP_033554192.1 DNA topoisomerase IV subunit B ParE NA NA NA core AMR POINT
Sample5 tir type III secretion system LEE translocated intimin receptor Tir NA NA 100 97.96 538 538 538 NODE_9_length_234966_cov_12.9153 41663 43276 \(+\) CAI43867.1 type III secretion system LEE translocated intimin receptor Tir NA NA NA plus VIRULENCE VIRULENCE
Sample5 uhpT_E350Q Escherichia fosfomycin resistant UhpT FOSFOMYCIN FOSFOMYCIN 100 97.84 463 463 463 NODE_7_length_258688_cov_13.1509 78038 79426 \(+\) WP_000879194.1 hexose phosphate transporter UhpT NA NA NA core AMR POINT


Sample7

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample7 lsa(A) ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE/STREPTOGRAMIN LINCOSAMIDE/STREPTOGRAMIN 100 99.6 498 498 498 10 103585 105078 \(+\) WP_002365053.1 ABC-F type ribosomal protection protein Lsa(A) NA NA NA core AMR AMR


Sample8

Sample Gene Sequence.Name Antibiotic.class Antibiotic.subclass Coverage Identity Target.Length Reference.Length Alignment.Length Contig Start Stop Strand Accession Clostest.sequence.name HMM.ID HMM.Description Protein.identifier Scope Element.type Element.Subtype
Sample8 clpL ATP-dependent protease ClpL NA NA 100 98.86 704 704 704 19 1511 3622 \(-\) ADB69780.1 ATP-dependent protease ClpL NA NA NA plus STRESS HEAT
Sample8 lsa(A) ABC-F type ribosomal protection protein Lsa(A) LINCOSAMIDE/STREPTOGRAMIN LINCOSAMIDE/STREPTOGRAMIN 100 99.00 498 498 498 8 35869 37362 \(-\) WP_002398829.1 ABC-F type ribosomal protection protein Lsa(A) NA NA NA core AMR AMR


NCBI

Sample1

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample1 aph(3’)-VI AMIKACIN;KANAMYCIN 100 100.00 NODE_56_length_10210_cov_22.632192 8272 9051 \(+\) 1-780/780 0/0 NG_051730.1 APH(3’)-VI family aminoglycoside O-phosphotransferase
Sample1 armA GENTAMICIN 100 100.00 NODE_60_length_7576_cov_19.451527 6514 7287 \(-\) 1-774/774 0/0 NG_047476.1 ArmA family 16S rRNA (guanine(1405)-N(7))-methyltransferase
Sample1 blaKPC-3 CARBAPENEM 100 100.00 NODE_45_length_23679_cov_20.948606 14049 14930 \(+\) 1-882/882 0/0 NG_049257.1 carbapenem-hydrolyzing class A beta-lactamase KPC-3
Sample1 blaNDM-1 CARBAPENEM 100 100.00 NODE_84_length_3546_cov_28.774575 2466 3278 \(-\) 1-813/813 0/0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1
Sample1 blaOXA-9 BETA-LACTAM 100 99.88 NODE_89_length_2852_cov_17.139459 244 1068 \(+\) 1-825/825 0/0 NG_049830.1 oxacillin-hydrolyzing class D beta-lactamase OXA-9
Sample1 blaSHV-187 BETA-LACTAM 100 99.54 NODE_85_length_3522_cov_41.898403 20 886 \(-\) 1-867/867 0/0 NG_050053.1 class A beta-lactamase SHV-187
Sample1 blaTEM-1 BETA-LACTAM 100 99.77 NODE_89_length_2852_cov_17.139459 1768 2628 \(+\) 1-861/861 0/0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1
Sample1 ble-MBL BLEOMYCIN 100 100.00 NODE_84_length_3546_cov_28.774575 2097 2462 \(-\) 1-366/366 0/0 NG_047559.1 bleomycin binding protein Ble-MBL
Sample1 dfrA5 TRIMETHOPRIM 100 100.00 NODE_82_length_3659_cov_26.867113 1429 1902 \(+\) 1-474/474 0/0 NG_051699.1 trimethoprim-resistant dihydrofolate reductase DfrA5
Sample1 fosA6 FOSFOMYCIN 100 98.33 NODE_14_length_151513_cov_31.882346 135672 136091 \(-\) 1-420/420 0/0 NG_051497.1 fosfomycin resistance glutathione transferase FosA6
Sample1 mph(A) MACROLIDE 100 98.71 NODE_68_length_6118_cov_26.757987 147 1077 \(+\) 1-921/921 2/10 NG_047986.1 Mph(A) family macrolide 2’-phosphotransferase
Sample1 mph(E) MACROLIDE 100 100.00 NODE_60_length_7576_cov_19.451527 1800 2684 \(-\) 1-885/885 0/0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase
Sample1 msr(E) MACROLIDE 100 100.00 NODE_60_length_7576_cov_19.451527 2740 4215 \(-\) 1-1476/1476 0/0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E)
Sample1 oqxA4 PHENICOL;QUINOLONE 100 100.00 NODE_17_length_122842_cov_28.181868 64068 65243 \(+\) 1-1176/1176 0/0 NG_050422.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA4
Sample1 oqxB12 PHENICOL;QUINOLONE 100 99.97 NODE_17_length_122842_cov_28.181868 65267 68419 \(+\) 1-3153/3153 0/0 NG_050430.1 multidrug efflux RND transporter permease subunit OqxB12
Sample1 qnrS1 QUINOLONE 100 100.00 NODE_56_length_10210_cov_22.632192 3738 4394 \(+\) 1-657/657 0/0 NG_050543.1 quinolone resistance pentapeptide repeat protein QnrS1
Sample1 sul1 SULFONAMIDE 100 100.00 NODE_82_length_3659_cov_26.867113 2427 3266 \(+\) 1-840/840 0/0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1
Sample1 sul2 SULFONAMIDE 100 100.00 NODE_67_length_6209_cov_27.717221 3883 4698 \(-\) 1-816/816 0/0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2


Sample2

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample2 aadA1 STREPTOMYCIN 100 99.87 NODE_59_length_8503_cov_27.463684 1271 2059 \(+\) 1-789/789 0/0 NG_047327.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1
Sample2 ant(2’’)-Ia GENTAMICIN;KANAMYCIN;TOBRAMYCIN 100 100.00 NODE_59_length_8503_cov_27.463684 680 1213 \(+\) 1-534/534 0/0 NG_047387.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia
Sample2 armA GENTAMICIN 100 100.00 NODE_66_length_5980_cov_31.768592 273 1046 \(+\) 1-774/774 0/0 NG_047476.1 ArmA family 16S rRNA (guanine(1405)-N(7))-methyltransferase
Sample2 blaKPC-3 CARBAPENEM 100 100.00 NODE_48_length_21954_cov_52.979888 17158 18039 \(+\) 1-882/882 0/0 NG_049257.1 carbapenem-hydrolyzing class A beta-lactamase KPC-3
Sample2 blaSHV-212 BETA-LACTAM 100 99.88 NODE_13_length_143880_cov_22.251622 115086 115946 \(+\) 1-861/861 0/0 NG_062284.1 class A beta-lactamase SHV-212
Sample2 catA1 CHLORAMPHENICOL 100 99.85 NODE_87_length_1659_cov_21.879267 300 959 \(+\) 1-660/660 0/0 NG_047582.1 type A-1 chloramphenicol O-acetyltransferase
Sample2 fosA_gen FOSFOMYCIN 100 96.43 NODE_25_length_81436_cov_30.505341 66696 67115 \(-\) 1-420/420 0/0 NG_047881.1 FosA family fosfomycin resistance glutathione transferase
Sample2 mph(E) MACROLIDE 100 100.00 NODE_66_length_5980_cov_31.768592 4876 5760 \(+\) 1-885/885 0/0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase
Sample2 msr(E) MACROLIDE 100 100.00 NODE_66_length_5980_cov_31.768592 3345 4820 \(+\) 1-1476/1476 0/0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E)
Sample2 oqxA10 PHENICOL;QUINOLONE 100 99.75 NODE_24_length_84154_cov_26.506904 53666 54841 \(-\) 1-1176/1176 0/0 NG_050418.1 multidrug efflux RND transporter periplasmic adaptor subunit OqxA10
Sample2 oqxB17 PHENICOL;QUINOLONE 100 99.62 NODE_24_length_84154_cov_26.506904 50490 53642 \(-\) 1-3153/3153 0/0 NG_050435.1 multidrug efflux RND transporter permease subunit OqxB17
Sample2 sul1 SULFONAMIDE 100 100.00 NODE_59_length_8503_cov_27.463684 2564 3403 \(+\) 1-840/840 0/0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1


Sample3

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample3 blaI_of_Z BETA-LACTAM 95.54 98.35 NODE_89_length_3290_cov_522.302009 1 364 \(-\) 1-364/381 0/0 NG_047499.1 penicillinase repressor BlaI
Sample3 blaR1 BETA-LACTAM 100.00 97.27 NODE_89_length_3290_cov_522.302009 354 2111 \(-\) 1-1758/1758 0/0 NG_051774.1 beta-lactam sensor/signal transducer BlaR1
Sample3 blaZ BETA-LACTAM 100.00 100.00 NODE_89_length_3290_cov_522.302009 2218 3063 \(+\) 1-846/846 0/0 NG_047534.1 penicillin-hydrolyzing class A beta-lactamase BlaZ
Sample3 tet(38) TETRACYCLINE 100.00 99.56 NODE_87_length_3816_cov_82.890189 571 1923 \(-\) 1-1353/1353 0/0 NG_055983.1 tetracycline efflux MFS transporter Tet(38)


Sample7

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample7 dfrE TRIMETHOPRIM 100 97.58 1 436056 436550 \(-\) 1-495/495 0/0 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE
Sample7 lsa(A) LINCOSAMIDE;STREPTOGRAMIN 100 99.40 10 103585 105081 \(+\) 1-1497/1497 0/0 NG_047931.1 ABC-F type ribosomal protection protein Lsa(A)


Sample8

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample8 dfrE TRIMETHOPRIM 100 97.98 14 10353 10847 \(-\) 1-495/495 0/0 NG_055770.1 trimethoprim-resistant dihydrofolate reductase DfrE
Sample8 lsa(A) LINCOSAMIDE;STREPTOGRAMIN 100 98.60 8 35866 37362 \(-\) 1-1497/1497 0/0 NG_055640.1 ABC-F type ribosomal protection protein Lsa(A)


Megares

Sample1

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample1 ACRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 99.75 97.66 NODE_4_length_259554_cov_28.160970 164601 165794 \(-\) 1-1197/1197 2/3 MEG_400 NA
Sample1 AMPH Drugs:betalactams:Penicillin_binding_protein 100.00 99.22 NODE_4_length_259554_cov_28.160970 34668 35828 \(-\) 1-1161/1161 0/0 MEG_730 NA
Sample1 APH3-PRIME Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases 100.00 100.00 NODE_56_length_10210_cov_22.632192 8272 9051 \(+\) 1-780/780 0/0 MEG_1069 NA
Sample1 ARMA Drugs:Aminoglycosides:16S_rRNA_methyltransferases 100.00 100.00 NODE_60_length_7576_cov_19.451527 6514 7287 \(-\) 1-774/774 0/0 MEG_1120 NA
Sample1 ASMA Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator 100.00 99.18 NODE_2_length_385203_cov_24.836368 268771 270594 \(+\) 1-1824/1824 0/0 MEG_1179 NA
Sample1 BRP Drugs:Glycopeptides:Bleomycin_resistance_protein 100.00 100.00 NODE_84_length_3546_cov_28.774575 2097 2462 \(-\) 1-366/366 0/0 MEG_1477 NA
Sample1 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 99.27 NODE_24_length_99615_cov_37.725321 56065 57438 \(-\) 1-1374/1374 0/0 MEG_2115 NA
Sample1 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 99.71 NODE_24_length_99615_cov_37.725321 57435 58133 \(-\) 1-699/699 0/0 MEG_2116 NA
Sample1 DFRA Drugs:Trimethoprim:Dihydrofolate_reductase 100.00 100.00 NODE_82_length_3659_cov_26.867113 1429 1902 \(+\) 1-474/474 0/0 MEG_2546 NA
Sample1 FOSA Drugs:Fosfomycin:Fosfomycin_thiol_transferases 100.00 98.33 NODE_14_length_151513_cov_31.882346 135672 136091 \(-\) 1-420/420 0/0 MEG_2987 NA
Sample1 KDEA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.68 NODE_13_length_161606_cov_24.101585 99195 100427 \(+\) 1-1233/1233 0/0 MEG_3447 NA
Sample1 KMRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.47 NODE_8_length_178368_cov_20.715785 81451 82950 \(-\) 1-1500/1500 0/0 MEG_3460 NA
Sample1 KPC Drugs:betalactams:Class_A_betalactamases 100.00 99.90 NODE_45_length_23679_cov_20.948606 14022 14987 \(+\) 1-966/966 0/0 MEG_3507 NA
Sample1 KPN Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.57 NODE_17_length_122842_cov_28.181868 113347 114519 \(+\) 1-1173/1173 0/0 MEG_3512 NA
Sample1 KPNE Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 100.00 NODE_11_length_169370_cov_33.859728 156970 157332 \(+\) 1-363/363 0/0 MEG_3514 NA
Sample1 KPNF Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 100.00 NODE_11_length_169370_cov_33.859728 157319 157648 \(+\) 1-330/330 0/0 MEG_3515 NA
Sample1 KPNO Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 99.91 NODE_2_length_385203_cov_24.836368 127559 128656 \(+\) 1-1098/1098 0/0 MEG_3516 NA
Sample1 MPHA Drugs:MLS:Macrolide_phosphotransferases 100.00 98.71 NODE_68_length_6118_cov_26.757987 147 1077 \(+\) 1-921/921 2/10 MEG_4030 NA
Sample1 MPHE Drugs:MLS:Macrolide_phosphotransferases 100.00 100.00 NODE_60_length_7576_cov_19.451527 1800 2684 \(-\) 1-885/885 0/0 MEG_4044 NA
Sample1 MSRE Drugs:MLS:MLS_resistance_ABC_efflux_pumps 100.00 100.00 NODE_60_length_7576_cov_19.451527 2740 4215 \(-\) 1-1476/1476 0/0 MEG_4075 NA
Sample1 NDM Drugs:betalactams:Class_B_betalactamases 100.00 100.00 NODE_84_length_3546_cov_28.774575 2466 3278 \(-\) 1-813/813 0/0 MEG_4143 NA
Sample1 OMP37 Drugs:betalactams:Mutant_porin_proteins 100.00 99.29 NODE_10_length_171959_cov_23.219686 134541 135665 \(+\) 1-1125/1125 0/0 MEG_4283 NA
Sample1 OQXA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 100.00 NODE_17_length_122842_cov_28.181868 64068 65243 \(+\) 1-1176/1176 0/0 MEG_4328 NA
Sample1 OQXB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 99.97 NODE_17_length_122842_cov_28.181868 65267 68419 \(+\) 1-3153/3153 0/0 MEG_4352 NA
Sample1 OXA Drugs:betalactams:Class_D_betalactamases 100.00 99.88 NODE_89_length_2852_cov_17.139459 229 1068 \(+\) 1-840/840 0/0 MEG_4757 NA
Sample1 PHOR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_regulator 100.00 99.66 NODE_35_length_49841_cov_21.565549 10350 11816 \(-\) 1-1467/1467 0/0 MEG_5786 NA
Sample1 QNRS Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr 100.00 100.00 NODE_56_length_10210_cov_22.632192 3738 4394 \(+\) 1-657/657 0/0 MEG_6020 NA
Sample1 SHV Drugs:betalactams:Class_A_betalactamases 97.57 99.35 NODE_85_length_3522_cov_41.898403 1 923 \(-\) 6-928/946 0/0 MEG_6473 NA
Sample1 SULI Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases 100.00 100.00 NODE_82_length_3659_cov_26.867113 2426 3393 \(+\) 1-968/968 0/0 MEG_6615 NA
Sample1 SULII Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases 100.00 100.00 NODE_67_length_6209_cov_27.717221 3883 4698 \(-\) 1-816/816 0/0 MEG_6617 NA
Sample1 TEM Drugs:betalactams:Class_A_betalactamases 98.26 99.44 NODE_89_length_2852_cov_17.139459 1401 2646 \(+\) 1-1246/1268 0/0 MEG_6875 NA


Sample2

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample2 ACRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 99.75 97.74 NODE_1_length_492243_cov_27.186120 163815 165008 \(-\) 1-1197/1197 2/3 MEG_400 NA
Sample2 AMPH Drugs:betalactams:Penicillin_binding_protein 100.00 99.14 NODE_1_length_492243_cov_27.186120 33962 35122 \(-\) 1-1161/1161 0/0 MEG_730 NA
Sample2 ANT2-DPRIME Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases 100.00 99.27 NODE_59_length_8503_cov_27.463684 530 1213 \(+\) 1-681/681 1/3 MEG_757 NA
Sample2 ANT3-DPRIME Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases 96.15 99.63 NODE_59_length_8503_cov_27.463684 1261 2059 \(+\) 30-831/831 1/3 MEG_915 NA
Sample2 ARMA Drugs:Aminoglycosides:16S_rRNA_methyltransferases 100.00 100.00 NODE_66_length_5980_cov_31.768592 273 1046 \(+\) 1-774/774 0/0 MEG_1120 NA
Sample2 ASMA Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator 100.00 99.67 NODE_5_length_274168_cov_25.481555 271983 273806 \(+\) 1-1824/1824 0/0 MEG_1179 NA
Sample2 CATA Drugs:Phenicol:Chloramphenicol_acetyltransferases 100.00 100.00 NODE_87_length_1659_cov_21.879267 289 959 \(+\) 1-671/671 0/0 MEG_1593 NA
Sample2 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 100.00 NODE_20_length_99576_cov_33.391240 41486 42184 \(+\) 1-699/699 0/0 MEG_2116 NA
Sample2 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 99.78 NODE_20_length_99576_cov_33.391240 42181 43554 \(+\) 1-1374/1374 0/0 MEG_2115 NA
Sample2 FOSA Drugs:Fosfomycin:Fosfomycin_thiol_transferases 100.00 96.43 NODE_25_length_81436_cov_30.505341 66696 67115 \(-\) 1-420/420 0/0 MEG_2991 NA
Sample2 KDEA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.59 NODE_26_length_79693_cov_24.311143 71256 72488 \(+\) 1-1233/1233 0/0 MEG_3447 NA
Sample2 KMRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.47 NODE_3_length_293842_cov_21.828965 160268 161767 \(-\) 1-1500/1500 0/0 MEG_3460 NA
Sample2 KPC Drugs:betalactams:Class_A_betalactamases 100.00 99.90 NODE_48_length_21954_cov_52.979888 17131 18096 \(+\) 1-966/966 0/0 MEG_3507 NA
Sample2 KPN Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 99.32 NODE_24_length_84154_cov_26.506904 8629 9801 \(-\) 1-1173/1173 0/0 MEG_3512 NA
Sample2 KPNE Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 99.45 NODE_36_length_39918_cov_22.269973 12038 12400 \(-\) 1-363/363 0/0 MEG_3514 NA
Sample2 KPNF Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 99.39 NODE_36_length_39918_cov_22.269973 11722 12051 \(-\) 1-330/330 0/0 MEG_3515 NA
Sample2 KPNO Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps 100.00 99.37 NODE_5_length_274168_cov_25.481555 129355 130458 \(+\) 1-1098/1098 1/6 MEG_3516 NA
Sample2 MPHE Drugs:MLS:Macrolide_phosphotransferases 100.00 100.00 NODE_66_length_5980_cov_31.768592 4876 5760 \(+\) 1-885/885 0/0 MEG_4044 NA
Sample2 MSRE Drugs:MLS:MLS_resistance_ABC_efflux_pumps 100.00 100.00 NODE_66_length_5980_cov_31.768592 3345 4820 \(+\) 1-1476/1476 0/0 MEG_4075 NA
Sample2 OMP37 Drugs:betalactams:Mutant_porin_proteins 99.82 99.38 NODE_14_length_143663_cov_23.334754 40622 41744 \(-\) 1-1123/1125 0/0 MEG_4283 NA
Sample2 OQXA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 99.75 NODE_24_length_84154_cov_26.506904 53666 54841 \(-\) 1-1176/1176 0/0 MEG_4326 NA
Sample2 OQXB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 99.62 NODE_24_length_84154_cov_26.506904 50490 53642 \(-\) 1-3153/3153 0/0 MEG_4350 NA
Sample2 PHOR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_regulator 100.00 99.59 NODE_8_length_202783_cov_22.745040 38907 40373 \(+\) 1-1467/1467 0/0 MEG_5786 NA
Sample2 SHV Drugs:betalactams:Class_A_betalactamases 99.70 98.61 NODE_13_length_143880_cov_22.251622 115040 116043 \(+\) 1-1004/1007 0/0 MEG_6428 NA
Sample2 SULI Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases 100.00 100.00 NODE_59_length_8503_cov_27.463684 2563 3530 \(+\) 1-968/968 0/0 MEG_6615 NA


Sample3

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample3 AAC3 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases 100.00 98.87 NODE_62_length_9585_cov_71.834208 2789 3232 \(+\) 1-444/444 0/0 MEG_47 NA
Sample3 AAC3 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases 100.00 98.87 NODE_62_length_9585_cov_71.834208 6354 6797 \(-\) 1-444/444 0/0 MEG_47 NA
Sample3 APH3-PRIME Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases 100.00 99.38 NODE_4_length_124164_cov_55.531573 36344 37144 \(+\) 1-801/801 0/0 MEG_1060 NA
Sample3 ARLR Drugs:Multi-drug_resistance:MDR_regulator 100.00 99.39 NODE_9_length_69056_cov_41.001174 15480 16139 \(+\) 1-660/660 0/0 MEG_1114 NA
Sample3 ARLS Drugs:Multi-drug_resistance:MDR_regulator 100.00 98.82 NODE_9_length_69056_cov_41.001174 16136 17491 \(+\) 1-1356/1356 0/0 MEG_1118 NA
Sample3 BLAI Drugs:betalactams:Penicillin_binding_protein_regulator 95.54 98.35 NODE_89_length_3290_cov_522.302009 1 364 \(-\) 1-364/381 0/0 MEG_1287 NA
Sample3 BLAR Drugs:betalactams:Penicillin_binding_protein_regulator 100.00 97.27 NODE_89_length_3290_cov_522.302009 354 2111 \(-\) 1-1758/1758 0/0 MEG_1299 NA
Sample3 BLAZ Drugs:betalactams:Class_A_betalactamases 100.00 99.21 NODE_89_length_3290_cov_522.302009 2176 3063 \(+\) 1-888/888 0/0 MEG_1409 NA
Sample3 DHAP Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps 100.00 98.48 NODE_6_length_102568_cov_74.986460 25025 26212 \(+\) 1-1188/1188 0/0 MEG_2614 NA
Sample3 LMRS Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 99.93 91.33 NODE_69_length_8519_cov_70.341210 1648 3089 \(-\) 2-1443/1443 0/0 MEG_3599 NA
Sample3 MEPA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps 100.00 98.69 NODE_7_length_75822_cov_72.897277 33734 35104 \(+\) 1-1371/1371 0/0 MEG_3834 NA
Sample3 MEPR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_regulator 100.00 98.81 NODE_7_length_75822_cov_72.897277 33223 33642 \(+\) 1-420/420 0/0 MEG_3836 NA
Sample3 MGRA Drugs:Multi-drug_resistance:MDR_regulator 100.00 99.55 NODE_5_length_123125_cov_66.683578 6450 6893 \(-\) 1-444/444 0/0 MEG_3943 NA
Sample3 MGRA Drugs:Multi-drug_resistance:MDR_regulator 100.00 99.55 NODE_5_length_123125_cov_66.683578 116233 116676 \(+\) 1-444/444 0/0 MEG_3943 NA
Sample3 NORA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 100.00 NODE_5_length_123125_cov_66.683578 14544 15710 \(+\) 1-1167/1167 0/0 MEG_4209 NA
Sample3 NORA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 100.00 NODE_5_length_123125_cov_66.683578 107416 108582 \(-\) 1-1167/1167 0/0 MEG_4209 NA
Sample3 RLMH Drugs:MLS:23S_rRNA_methyltransferases 100.00 98.12 NODE_29_length_32051_cov_87.623734 30390 30869 \(+\) 1-480/480 0/0 MEG_6058 NA
Sample3 TET38 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps 100.00 99.56 NODE_87_length_3816_cov_82.890189 571 1923 \(-\) 1-1353/1353 0/0 MEG_6981 NA


Sample4

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample4 LMRP Drugs:Multi-drug_resistance:Multi-drug_MFS_efflux_pumps 99.92 98.85 3 94557 95776 \(-\) 1-1220/1221 0/0 MEG_3598 NA


Sample5

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample5 ACRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 91.79 NODE_1_length_833323_cov_12.8744 605819 607012 \(+\) 1-1194/1194 0/0 MEG_399 NA
Sample5 ACRB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps 100.00 92.29 NODE_1_length_833323_cov_12.8744 607035 610184 \(+\) 1-3150/3150 0/0 MEG_401 NA
Sample5 BACA Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase 99.76 93.05 NODE_2_length_652771_cov_13.1584 206183 207002 \(+\) 1-820/822 0/0 MEG_1189 NA
Sample5 BAER Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator 100.00 91.42 NODE_4_length_290048_cov_13.1184 50678 51400 \(+\) 1-723/723 0/0 MEG_1192 NA
Sample5 BAES Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator 100.00 90.53 NODE_4_length_290048_cov_13.1184 49278 50681 \(+\) 1-1404/1404 0/0 MEG_1193 NA
Sample5 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 93.45 NODE_13_length_125154_cov_13.4191 71110 71811 \(+\) 1-699/699 1/3 MEG_2120 NA
Sample5 CPXAR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 99.56 91.67 NODE_13_length_125154_cov_13.4191 71808 73175 \(+\) 1-1368/1374 0/0 MEG_2121 NA
Sample5 CRP Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator 100.00 94.79 NODE_8_length_237146_cov_13.3532 42294 42926 \(+\) 1-633/633 0/0 MEG_2132 NA
Sample5 EMRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 95.23 NODE_20_length_91953_cov_12.8135 65767 66939 \(+\) 1-1173/1173 0/0 MEG_2722 NA
Sample5 EMRB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps 100.00 94.87 NODE_20_length_91953_cov_12.8135 66956 68494 \(+\) 1-1539/1539 0/0 MEG_2725 NA
Sample5 EMRR Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator 100.00 95.10 NODE_20_length_91953_cov_12.8135 65110 65640 \(+\) 1-531/531 0/0 MEG_2734 NA
Sample5 HNS Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps 100.00 94.69 NODE_5_length_284821_cov_12.9843 172459 172872 \(+\) 1-414/414 0/0 MEG_3271 NA
Sample5 KDPE Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps 100.00 90.56 NODE_1_length_833323_cov_12.8744 406581 407258 \(+\) 1-678/678 0/0 MEG_3448 NA
Sample5 MDTA Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps 100.00 93.67 NODE_4_length_290048_cov_13.1184 40427 41674 \(+\) 1-1248/1248 0/0 MEG_3746 NA
Sample5 MDTB Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps 100.00 92.60 NODE_4_length_290048_cov_13.1184 41674 44796 \(+\) 1-3123/3123 0/0 MEG_3747 NA
Sample5 MDTC Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps 100.00 90.90 NODE_4_length_290048_cov_13.1184 44797 47874 \(+\) 1-3078/3078 0/0 MEG_3749 NA
Sample5 PBP2 Drugs:betalactams:Penicillin_binding_protein 100.00 91.17 NODE_1_length_833323_cov_12.8744 468361 470262 \(+\) 1-1902/1902 0/0 MEG_5400 NA
Sample5 ROBA Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps 100.00 92.30 NODE_6_length_267875_cov_13.459 30931 31800 \(-\) 1-870/870 0/0 MEG_6082 NA
Sample5 SOXS Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator 99.69 92.88 NODE_14_length_124664_cov_13.263 89571 89893 \(-\) 1-323/324 0/0 MEG_6551 NA


Sample7

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample7 DFRE Drugs:Trimethoprim:Dihydrofolate_reductase 100.00 97.58 1 436056 436550 \(-\) 1-495/495 0/0 MEG_2577 NA
Sample7 EFRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps 98.49 99.09 13 24720 26154 \(-\) 1-1436/1457 1/1 MEG_2706 NA
Sample7 EFRB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps 96.69 97.54 13 23022 24075 \(-\) 34-1085/1086 6/6 MEG_2707 NA
Sample7 LSA Drugs:MLS:MLS_resistance_ABC_efflux_pumps 100.00 99.40 10 103585 105081 \(+\) 1-1497/1497 0/0 MEG_3644 NA


Sample8

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample8 DFRE Drugs:Trimethoprim:Dihydrofolate_reductase 100.00 97.98 14 10353 10847 \(-\) 1-495/495 0/0 MEG_2577 NA
Sample8 EFRA Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps 98.49 99.03 11 24718 26152 \(-\) 1-1436/1457 1/1 MEG_2706 NA
Sample8 EFRB Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps 96.69 97.44 11 23020 24073 \(-\) 34-1085/1086 6/6 MEG_2707 NA
Sample8 LSA Drugs:MLS:MLS_resistance_ABC_efflux_pumps 100.00 98.60 8 35866 37362 \(-\) 1-1497/1497 0/0 MEG_3643 NA


ResFinder

Sample1

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample1 aph(3’)-VI_1 Amikacin 100 100.00 NODE_56_length_10210_cov_22.632192 8272 9051 \(+\) 1-780/780 0/0 KC170992 aph(3’)-VI
Sample1 armA_1 Amikacin;Gentamicin;Tobramycin 100 100.00 NODE_60_length_7576_cov_19.451527 6514 7287 \(-\) 1-774/774 0/0 AY220558 armA
Sample1 blaKPC-3_1 Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Aztreonam;Cefepime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam;Ticarcillin;Ticarcillin+Clavulanic_acid 100 100.00 NODE_45_length_23679_cov_20.948606 14049 14930 \(+\) 1-882/882 0/0 HM769262 blaKPC-3
Sample1 blaNDM-1_1 Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Cefepime;Cefixime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam 100 100.00 NODE_84_length_3546_cov_28.774575 2466 3278 \(-\) 1-813/813 0/0 FN396876 blaNDM-1
Sample1 blaOXA-9_1 Amoxicillin;Ampicillin 100 99.88 NODE_89_length_2852_cov_17.139459 244 1068 \(+\) 1-825/825 0/0 KQ089875 blaOXA-9
Sample1 blaSHV-187_1 100 99.54 NODE_85_length_3522_cov_41.898403 20 886 \(-\) 1-867/867 0/0 LN515533 blaSHV-187
Sample1 blaTEM-1A_1 Amoxicillin;Ampicillin;Cephalothin;Piperacillin;Ticarcillin 100 99.88 NODE_89_length_2852_cov_17.139459 1768 2628 \(+\) 1-861/861 0/0 HM749966 blaTEM-1A
Sample1 dfrA5_1 Trimethoprim 100 100.00 NODE_82_length_3659_cov_26.867113 1429 1902 \(+\) 1-474/474 0/0 X12868 dfrA5
Sample1 fosA6_1 Fosfomycin 97 98.33 NODE_14_length_151513_cov_31.882346 135672 136091 \(-\) 1-420/433 0/0 KU254579 fosA6
Sample1 mph(A)_2 Erythromycin;Azithromycin;Spiramycin;Telithromycin 100 98.71 NODE_68_length_6118_cov_26.757987 147 1077 \(+\) 1-921/921 2/10 U36578 mph(A)
Sample1 mph(E)_1 Erythromycin 100 100.00 NODE_60_length_7576_cov_19.451527 1800 2684 \(-\) 1-885/885 0/0 DQ839391 mph(E)
Sample1 msr(E)_1 100 100.00 NODE_60_length_7576_cov_19.451527 2740 4215 \(-\) 1-1476/1476 0/0 FR751518 msr(E)
Sample1 oqxA_1 Nalidixic_acid;Ciprofloxacin 100 99.15 NODE_17_length_122842_cov_28.181868 64068 65243 \(+\) 1-1176/1176 0/0 EU370913 oqxA
Sample1 oqxB_1 Nalidixic_acid;Ciprofloxacin 100 98.95 NODE_17_length_122842_cov_28.181868 65267 68419 \(+\) 1-3153/3153 0/0 EU370913 oqxB
Sample1 qnrS1_1 Ciprofloxacin 100 100.00 NODE_56_length_10210_cov_22.632192 3738 4394 \(+\) 1-657/657 0/0 AB187515 qnrS1
Sample1 sul1_5 Sulfamethoxazole 100 99.89 NODE_82_length_3659_cov_26.867113 2400 3266 \(+\) 1-867/867 0/0 EU780013 sul1
Sample1 sul2_2 Sulfamethoxazole 100 100.00 NODE_67_length_6209_cov_27.717221 3883 4698 \(-\) 1-816/816 0/0 AY034138 sul2


Sample2

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample2 ant(2’’)-Ia_1 Gentamicin;Tobramycin 100 100.00 NODE_59_length_8503_cov_27.463684 680 1213 \(+\) 1-534/534 0/0 X04555 ant(2’’)-Ia
Sample2 armA_1 Amikacin;Gentamicin;Tobramycin 100 100.00 NODE_66_length_5980_cov_31.768592 273 1046 \(+\) 1-774/774 0/0 AY220558 armA
Sample2 blaKPC-3_1 Amoxicillin;Amoxicillin+Clavulanic_acid;Ampicillin;Ampicillin+Clavulanic_acid;Aztreonam;Cefepime;Cefotaxime;Cefoxitin;Ceftazidime;Ertapenem;Imipenem;Meropenem;Piperacillin;Piperacillin+Tazobactam;Ticarcillin;Ticarcillin+Clavulanic_acid 100 100.00 NODE_48_length_21954_cov_52.979888 17158 18039 \(+\) 1-882/882 0/0 HM769262 blaKPC-3
Sample2 blaSHV-106_1 Amoxicillin;Ampicillin;Aztreonam;Cefepime;Cefotaxime;Ceftazidime;Ceftriaxone;Piperacillin;Ticarcillin 100 99.77 NODE_13_length_143880_cov_22.251622 115086 115946 \(+\) 1-861/861 0/0 AM922307 blaSHV-106
Sample2 catA1_1 Chloramphenicol 100 99.85 NODE_87_length_1659_cov_21.879267 300 959 \(+\) 1-660/660 0/0 V00622 catA1
Sample2 fosA_6 Fosfomycin 100 96.43 NODE_25_length_81436_cov_30.505341 66696 67115 \(-\) 1-420/420 0/0 ACZD01000244 fosA
Sample2 mph(E)_1 Erythromycin 100 100.00 NODE_66_length_5980_cov_31.768592 4876 5760 \(+\) 1-885/885 0/0 DQ839391 mph(E)
Sample2 msr(E)_1 100 100.00 NODE_66_length_5980_cov_31.768592 3345 4820 \(+\) 1-1476/1476 0/0 FR751518 msr(E)
Sample2 oqxA_1 Nalidixic_acid;Ciprofloxacin 100 99.66 NODE_24_length_84154_cov_26.506904 53666 54841 \(-\) 1-1176/1176 0/0 EU370913 oqxA
Sample2 oqxB_1 Nalidixic_acid;Ciprofloxacin 100 98.83 NODE_24_length_84154_cov_26.506904 50490 53642 \(-\) 1-3153/3153 0/0 EU370913 oqxB
Sample2 sul1_5 Sulfamethoxazole 100 99.89 NODE_59_length_8503_cov_27.463684 2537 3403 \(+\) 1-867/867 0/0 EU780013 sul1


Sample3

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample3 blaZ_79 Amoxicillin;Ampicillin;Penicillin;Piperacillin 100 99.21 NODE_89_length_3290_cov_522.302009 2176 3063 \(+\) 1-888/888 0/0 KU607584 blaZ


Sample7

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample7 lsa(A)_1 Lincomycin;Clindamycin;Dalfopristin;Pristinamycin_IIA;Virginiamycin_M 100 99.4 10 103585 105081 \(+\) 1-1497/1497 0/0 AY225127 lsa(A)


Sample8

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample8 lsa(A)_3 Lincomycin;Clindamycin;Dalfopristin;Pristinamycin_IIA;Virginiamycin_M 100 98.4 8 35866 37362 \(-\) 1-1497/1497 0/0 AY737526 lsa(A)


CARD

Sample1

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample1 APH(3’)-VI aminoglycoside 100.00 100.00 NODE_56_length_10210_cov_22.632192 8272 9051 \(+\) 1-780/780 0/0 KC170992.1:8362-9142 APH(3’)-VI is an aminoglycoside phosphoryltransferase that acts on the 3-OH of target of aminoglycosides.
Sample1 armA aminoglycoside 100.00 100.00 NODE_60_length_7576_cov_19.451527 6514 7287 \(-\) 1-774/774 0/0 GU437214.1:0-774 ArmA is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site.
Sample1 determinant_of_bleomycin_resistance glycopeptide 100.00 100.00 NODE_84_length_3546_cov_28.774575 2097 2462 \(-\) 1-366/366 0/0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region.
Sample1 dfrA5 diaminopyrimidine 100.00 100.00 NODE_82_length_3659_cov_26.867113 1429 1902 \(+\) 1-474/474 0/0 DQ278190:0-474 dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae
Sample1 FosA6 fosfomycin 100.00 98.33 NODE_14_length_151513_cov_31.882346 135672 136091 \(-\) 1-420/420 0/0 KU254579.1:59421-59841 fosA6 is a plasmid-encoded enzyme that confers resistance to fosfomycin in Escherichia coli by breaking the epoxide ring of the molecule.
Sample1 Klebsiella_pneumoniae_acrA cephalosporin;fluoroquinolone;glycylcycline;penam;phenicol;rifamycin;tetracycline;triclosan 99.75 97.66 NODE_4_length_259554_cov_28.160970 164601 165794 \(-\) 1-1197/1197 2/3 AJ318073.1:793-1990 AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.
Sample1 Klebsiella_pneumoniae_KpnE aminoglycoside;cephalosporin;macrolide;peptide;rifamycin;tetracycline 100.00 100.00 NODE_11_length_169370_cov_33.859728 156970 157332 \(+\) 1-363/363 0/0 AP006725.1:2483889-2484252 KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan
Sample1 Klebsiella_pneumoniae_KpnF aminoglycoside;cephalosporin;macrolide;peptide;rifamycin;tetracycline 100.00 100.00 NODE_11_length_169370_cov_33.859728 157319 157648 \(+\) 1-330/330 0/0 AP006725.1:2484238-2484568 KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.
Sample1 Klebsiella_pneumoniae_KpnG aminoglycoside;carbapenem;cephalosporin;fluoroquinolone;macrolide;penam;penem;peptide 100.00 99.57 NODE_17_length_122842_cov_28.181868 113347 114519 \(+\) 1-1173/1173 0/0 ACWO01000051.1:22092-23265 KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin
Sample1 Klebsiella_pneumoniae_OmpK37 carbapenem;cephalosporin;cephamycin;monobactam;penam;penem 100.00 99.29 NODE_10_length_171959_cov_23.219686 134541 135665 \(+\) 1-1125/1125 0/0 AJ011502.1:300-1425 Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain beta-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.
Sample1 KPC-3 carbapenem;cephalosporin;monobactam;penam 100.00 100.00 NODE_45_length_23679_cov_20.948606 14049 14930 \(+\) 1-882/882 0/0 AF395881:0-882 KPC-3 is a beta-lactamase found in Klebsiella pneumoniae
Sample1 mphA macrolide 99.67 100.00 NODE_68_length_6118_cov_26.757987 147 1049 \(+\) 1-903/906 0/0 D16251.1:2531-1625 The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner.
Sample1 mphE macrolide 100.00 100.00 NODE_60_length_7576_cov_19.451527 1800 2684 \(-\) 1-885/885 0/0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105
Sample1 msrE lincosamide;macrolide;oxazolidinone;phenicol;pleuromutilin;streptogramin;tetracycline 100.00 100.00 NODE_60_length_7576_cov_19.451527 2740 4215 \(-\) 1-1476/1476 0/0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species.
Sample1 NDM-1 carbapenem;cephalosporin;cephamycin;penam 100.00 100.00 NODE_84_length_3546_cov_28.774575 2466 3278 \(-\) 1-813/813 0/0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics.
Sample1 oqxA diaminopyrimidine;fluoroquinolone;glycylcycline;nitrofuran;tetracycline 100.00 99.15 NODE_17_length_122842_cov_28.181868 64068 65243 \(+\) 1-1176/1176 0/0 EU370913.1:46651-47827 RND efflux pump conferring resistance to fluoroquinolone
Sample1 oqxB diaminopyrimidine;fluoroquinolone;glycylcycline;nitrofuran;tetracycline 100.00 98.95 NODE_17_length_122842_cov_28.181868 65267 68419 \(+\) 1-3153/3153 0/0 EU370913.1:47850-51003 RND efflux pump conferring resistance to fluoroquinolone
Sample1 OXA-9 cephalosporin;penam 100.00 99.88 NODE_89_length_2852_cov_17.139459 244 1068 \(+\) 1-825/825 0/0 M55547:0-825 OXA-9 is a beta-lactamase found in Klebsiella pneumoniae.
Sample1 QnrS1 fluoroquinolone 100.00 100.00 NODE_56_length_10210_cov_22.632192 3738 4394 \(+\) 1-657/657 0/0 DQ485529.1:0-657 QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri
Sample1 SHV-187 carbapenem;cephalosporin;penam 100.00 99.54 NODE_85_length_3522_cov_41.898403 20 886 \(-\) 1-867/867 0/0 LN515533:0-867 From the Lahey list of beta-lactamases.
Sample1 sul1 sulfonamide 100.00 100.00 NODE_82_length_3659_cov_26.867113 2427 3266 \(+\) 1-840/840 0/0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.
Sample1 sul2 sulfonamide 100.00 100.00 NODE_67_length_6209_cov_27.717221 3883 4698 \(-\) 1-816/816 0/0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids.
Sample1 TEM-122 cephalosporin;monobactam;penam;penem 100.00 99.77 NODE_89_length_2852_cov_17.139459 1768 2628 \(+\) 1-861/861 0/0 AY307100:0-861 TEM-122 is an inhibitor-resistant beta-lactamase found in E. coli.


Sample2

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample2 ANT(2’’)-Ia aminoglycoside 100.00 100.00 NODE_59_length_8503_cov_27.463684 680 1213 \(+\) 1-534/534 0/0 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii
Sample2 armA aminoglycoside 100.00 100.00 NODE_66_length_5980_cov_31.768592 273 1046 \(+\) 1-774/774 0/0 GU437214.1:0-774 ArmA is a 16S rRNA methyltransferase that targets mature or nearly mature 30S subunits. It transfers a methyl group from S-adenosyl-L-methionine to N7-G1405 of the 16S rRNA an aminoglycoside binding site.
Sample2 catI phenicol 100.00 99.85 NODE_87_length_1659_cov_21.879267 300 959 \(+\) 1-660/660 0/0 V00622:243-903 catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii
Sample2 FosA5 fosfomycin 100.00 96.19 NODE_25_length_81436_cov_30.505341 66696 67115 \(-\) 1-420/420 0/0 KP143090.1:1619-1199 fosA5 is a fosfomycin resistance gene isolated from clinical strain of Escherichia coli E265. It is susceptible to amikacin tetracycline and imipenem and resistant to sulphonamide cephalosporins gentamicin ciprofloxacin chloramphenicol and streptomycin
Sample2 Klebsiella_pneumoniae_acrA cephalosporin;fluoroquinolone;glycylcycline;penam;phenicol;rifamycin;tetracycline;triclosan 99.75 97.74 NODE_1_length_492243_cov_27.186120 163815 165008 \(-\) 1-1197/1197 2/3 AJ318073.1:793-1990 AcrA is a subunit of the AcrAB multidrug efflux system that in K. pneumoniae which is encoded by the acrRAB operon.
Sample2 Klebsiella_pneumoniae_KpnE aminoglycoside;cephalosporin;macrolide;peptide;rifamycin;tetracycline 100.00 99.45 NODE_36_length_39918_cov_22.269973 12038 12400 \(-\) 1-363/363 0/0 AP006725.1:2483889-2484252 KpnE subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan
Sample2 Klebsiella_pneumoniae_KpnF aminoglycoside;cephalosporin;macrolide;peptide;rifamycin;tetracycline 100.00 99.39 NODE_36_length_39918_cov_22.269973 11722 12051 \(-\) 1-330/330 0/0 AP006725.1:2484238-2484568 KpnF subunit of KpnEF resembles EbrAB from E. coli. Mutation in KpnEF resulted in increased susceptibility to cefepime ceftriaxon colistin erythromycin rifampin tetracycline and streptomycin as well as enhanced sensitivity toward sodium dodecyl sulfate deoxycholate dyes benzalkonium chloride chlorhexidine and triclosan.
Sample2 Klebsiella_pneumoniae_KpnG aminoglycoside;carbapenem;cephalosporin;fluoroquinolone;macrolide;penam;penem;peptide 100.00 99.32 NODE_24_length_84154_cov_26.506904 8629 9801 \(-\) 1-1173/1173 0/0 ACWO01000051.1:22092-23265 KpnG consists of ~390 residues and resembles EmrA of E. coli. Disruption of the pump components KpnG-KpnH signficantly decrease resistance to azithromycin ceftazidime ciprofloxacin ertapenem erythromycin gentamicin imipenem ticarcillin norfloxacin polymyxin-B piperacillin spectinomycin tobramycin and streptomycin
Sample2 Klebsiella_pneumoniae_OmpK37 carbapenem;cephalosporin;cephamycin;monobactam;penam;penem 99.82 99.38 NODE_14_length_143663_cov_23.334754 40622 41744 \(-\) 1-1123/1125 0/0 AJ011502.1:300-1425 Klebsiella pneumoniae outer membrane porin protein. Is preferentially detected in porin-deficient strains. Functional characterization of this new porin revealed a narrower pore than those of porins OmpK35 and OmpK36 which did not allow penetration by certain beta-lactams. Also when a resistant strain expresses porin OmpK37 is less susceptible to cefotaxime and cefoxitin than when it is expressing either OmpK36 or OmpK35.
Sample2 KPC-3 carbapenem;cephalosporin;monobactam;penam 100.00 100.00 NODE_48_length_21954_cov_52.979888 17158 18039 \(+\) 1-882/882 0/0 AF395881:0-882 KPC-3 is a beta-lactamase found in Klebsiella pneumoniae
Sample2 mphE macrolide 100.00 100.00 NODE_66_length_5980_cov_31.768592 4876 5760 \(+\) 1-885/885 0/0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105
Sample2 msrE lincosamide;macrolide;oxazolidinone;phenicol;pleuromutilin;streptogramin;tetracycline 100.00 100.00 NODE_66_length_5980_cov_31.768592 3345 4820 \(+\) 1-1476/1476 0/0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species.
Sample2 oqxA diaminopyrimidine;fluoroquinolone;glycylcycline;nitrofuran;tetracycline 100.00 99.66 NODE_24_length_84154_cov_26.506904 53666 54841 \(-\) 1-1176/1176 0/0 EU370913.1:46651-47827 RND efflux pump conferring resistance to fluoroquinolone
Sample2 oqxB diaminopyrimidine;fluoroquinolone;glycylcycline;nitrofuran;tetracycline 100.00 98.83 NODE_24_length_84154_cov_26.506904 50490 53642 \(-\) 1-3153/3153 0/0 EU370913.1:47850-51003 RND efflux pump conferring resistance to fluoroquinolone
Sample2 SHV-106 carbapenem;cephalosporin;penam 100.00 99.77 NODE_13_length_143880_cov_22.251622 115086 115946 \(+\) 1-861/861 0/0 AM941847:0-861 SHV-106 is an extended-spectrum beta-lactamase that has been found in clinical isolates.
Sample2 sul1 sulfonamide 100.00 100.00 NODE_59_length_8503_cov_27.463684 2564 3403 \(+\) 1-840/840 0/0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons.


Sample3

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample3 arlR acridine_dye;fluoroquinolone 100.00 98.94 NODE_9_length_69056_cov_41.001174 15480 16139 \(+\) 1-660/660 0/0 CP023390.1:1462248-1461588 ArlR is a response regulator that binds to the norA promoter to activate expression. ArlR must first be phosphorylated by ArlS.
Sample3 arlS acridine_dye;fluoroquinolone 100.00 98.82 NODE_9_length_69056_cov_41.001174 16136 17491 \(+\) 1-1356/1356 0/0 CP000253.1:1361636-1360280 ArlS is a protein histidine kinase that phosphorylates ArlR a promoter for norA expression.
Sample3 mepA glycylcycline;tetracycline 100.00 98.67 NODE_7_length_75822_cov_72.897277 33749 35104 \(+\) 1-1356/1356 0/0 AY661734.1:839-2195 MepA is an efflux protein regulated by MepR and part of the MepRAB cluster. Its presence in Staphylococcus aureus led to multidrug resistance while it has also been shown to decrease tigecycline susceptibility.
Sample3 mepR glycylcycline;tetracycline 100.00 98.81 NODE_7_length_75822_cov_72.897277 33223 33642 \(+\) 1-420/420 0/0 BA000017.4:379931-380351 MepR is an upstream repressor of MepA in Staphylococcus aureus. It is part of the mepRAB operon.
Sample3 mgrA acridine_dye;cephalosporin;fluoroquinolone;penam;peptide;tetracycline 100.00 99.55 NODE_5_length_123125_cov_66.683578 6450 6893 \(-\) 1-444/444 0/0 BA000018.3:735860-735416 MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38.
Sample3 mgrA acridine_dye;cephalosporin;fluoroquinolone;penam;peptide;tetracycline 100.00 99.55 NODE_5_length_123125_cov_66.683578 116233 116676 \(+\) 1-444/444 0/0 BA000018.3:735860-735416 MgrA also known as NorR is a regulator for norA norB and tet38. It is a positive regulator for norA expression but is a direct repressor for norB and an indirect repressor of tet38.
Sample3 PC1_beta-lactamase_(blaZ) penam 100.00 97.87 NODE_89_length_3290_cov_522.302009 2218 3063 \(+\) 1-846/846 0/0 CP000732.1:10528-9682 The blaZ beta-lactamase is found in Bacillus subtilis and Staphylococcus aureus.
Sample3 Staphylococcus_aureus_norA fluoroquinolone 99.91 91.25 NODE_5_length_123125_cov_66.683578 14544 15709 \(+\) 1-1166/1167 0/0 D90119.1:477-1644 NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli.
Sample3 Staphylococcus_aureus_norA fluoroquinolone 99.91 91.25 NODE_5_length_123125_cov_66.683578 107417 108582 \(-\) 1-1166/1167 0/0 D90119.1:477-1644 NorA gene cloned from Staphylococcus aureus conferred relatively high resistance to hydrophilic quinolones such as norfloxacin enoxacin ofloxacin and ciprofloxacin in S. aureus and Escherichia coli. Had low or no resistance at all to hydrophobic ones such as nalidixic acid oxolinic acid and sparfloxacin in S. aureus and Escherichia coli.
Sample3 Staphylococcys_aureus_LmrS aminoglycoside;diaminopyrimidine;macrolide;oxazolidinone;phenicol 99.93 91.33 NODE_69_length_8519_cov_70.341210 1648 3089 \(-\) 2-1443/1443 0/0 CP000046.1:2236817-2235374 MFS transporters are secondary active transporters with single-polypeptide chains containing 400-600 amino acids that transport small solutes across the membrane by using electrochemical gradients. LmrS has 14 transmembrane helices and when expressed in E. coli is capable of extruding a variety of antibiotics inclinding linezolid trimethoprim florfenicol chlorampheniocol erythromycin streptomycin kanamycin and fusidic acid
Sample3 tet(38) tetracycline 100.00 98.82 NODE_87_length_3816_cov_82.890189 571 1923 \(-\) 1-1353/1353 0/0 AY825285:0-1353 Tet38 is a tetracycline efflux pump found in the Gram-positive Staphylococcus aureus. It is regulated by mgrA which also regulates NorB.


Sample4

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample4 lmrP lincosamide;macrolide;streptogramin;tetracycline 99.92 98.85 3 94557 95776 \(-\) 1-1220/1221 0/0 CP000259.1:1770310-1769089 lmrP is a proton motive force-dependent drug transporter that is part of the MFS efflux pump family.


Sample5

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample5 acrB cephalosporin;fluoroquinolone;glycylcycline;penam;phenicol;rifamycin;tetracycline;triclosan 100.00 92.29 NODE_1_length_833323_cov_12.8744 607035 610184 \(+\) 1-3150/3150 0/0 U00096.3:484403-481253 Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter.
Sample5 bacA peptide 99.76 92.81 NODE_2_length_652771_cov_13.1584 206183 207002 \(+\) 1-820/822 0/0 U00096.3:3204131-3203309 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin.
Sample5 baeR aminocoumarin;aminoglycoside 100.00 91.42 NODE_4_length_290048_cov_13.1184 50678 51400 \(+\) 1-723/723 0/0 AP009048.1:2166412-2167135 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes.
Sample5 baeS aminocoumarin;aminoglycoside 100.00 90.53 NODE_4_length_290048_cov_13.1184 49278 50681 \(+\) 1-1404/1404 0/0 AP009048:2165012-2166416 BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance.
Sample5 cpxA aminocoumarin;aminoglycoside 99.56 91.59 NODE_13_length_125154_cov_13.4191 71808 73175 \(+\) 1-1368/1374 0/0 BA000007.3:4905062-4903688 CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression.
Sample5 CRP fluoroquinolone;macrolide;penam 100.00 94.79 NODE_8_length_237146_cov_13.3532 42294 42926 \(+\) 1-633/633 0/0 AP009048.1:4154296-4153663 CRP is a global regulator that represses MdtEF multidrug efflux pump expression.
Sample5 emrA fluoroquinolone 100.00 95.23 NODE_20_length_91953_cov_12.8135 65767 66939 \(+\) 1-1173/1173 0/0 AP009048:2810082-2811255 EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium.
Sample5 emrB fluoroquinolone 100.00 94.87 NODE_20_length_91953_cov_12.8135 66956 68494 \(+\) 1-1539/1539 0/0 U00096:2812615-2814154 emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin.
Sample5 emrR fluoroquinolone 100.00 95.10 NODE_20_length_91953_cov_12.8135 65110 65640 \(+\) 1-531/531 0/0 U00096.3:2810769-2811300 EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression.
Sample5 Escherichia_coli_acrA cephalosporin;fluoroquinolone;glycylcycline;penam;phenicol;rifamycin;tetracycline;triclosan 100.00 91.79 NODE_1_length_833323_cov_12.8744 605819 607012 \(+\) 1-1194/1194 0/0 U00096.3:485619-484425 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli.
Sample5 H-NS cephalosporin;cephamycin;fluoroquinolone;macrolide;penam;tetracycline 100.00 94.69 NODE_5_length_284821_cov_12.9843 172459 172872 \(+\) 1-414/414 0/0 BA000007.3:1738104-1737690 H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters.
Sample5 kdpE aminoglycoside 100.00 90.56 NODE_1_length_833323_cov_12.8744 406581 407258 \(+\) 1-678/678 0/0 U00096.3:721733-721055 kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding.
Sample5 mdtA aminocoumarin 100.00 93.67 NODE_4_length_290048_cov_13.1184 40427 41674 \(+\) 1-1248/1248 0/0 U00096:2154015-2155263 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC.
Sample5 mdtB aminocoumarin 100.00 92.60 NODE_4_length_290048_cov_13.1184 41674 44796 \(+\) 1-3123/3123 0/0 U00096:2155262-2158385 MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex.
Sample5 mdtC aminocoumarin 100.00 90.90 NODE_4_length_290048_cov_13.1184 44797 47874 \(+\) 1-3078/3078 0/0 U00096:2158385-2161463 MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58.
Sample5 tolC aminocoumarin;aminoglycoside;carbapenem;cephalosporin;cephamycin;fluoroquinolone;glycylcycline;macrolide;penam;penem;peptide;phenicol;rifamycin;tetracycline;triclosan 100.00 90.12 NODE_2_length_652771_cov_13.1584 233121 234608 \(-\) 1-1488/1488 0/0 FJ768952:0-1488 TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.


Sample7

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample7 dfrE diaminopyrimidine 100.00 97.58 1 436056 436550 \(-\) 1-495/495 0/0 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis
Sample7 efrA fluoroquinolone;macrolide;rifamycin 100.00 99.31 13 24634 26361 \(-\) 1-1728/1728 0/0 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance.
Sample7 efrB fluoroquinolone;macrolide;rifamycin 96.69 97.54 13 23022 24075 \(-\) 34-1085/1086 6/6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance.
Sample7 emeA acridine_dye 97.72 96.95 4 24799 25953 \(+\) 1-1182/1182 1/27 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine.
Sample7 lsaA lincosamide;macrolide;oxazolidinone;phenicol;pleuromutilin;streptogramin;tetracycline 100.00 99.40 10 103585 105081 \(+\) 1-1497/1497 0/0 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin.


Sample8

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample8 dfrE diaminopyrimidine 100.00 97.98 14 10353 10847 \(-\) 1-495/495 0/0 AIIS01000002.1:234307-233812 dfrE is a chromosome-encoded dihydrofolate reductase found in Enterococcus faecalis
Sample8 efrA fluoroquinolone;macrolide;rifamycin 100.00 99.77 11 24632 26359 \(-\) 1-1728/1728 0/0 NZ_PTWF01000025.1:35858-37586 efrA is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer drug resistance.
Sample8 efrB fluoroquinolone;macrolide;rifamycin 96.69 97.44 11 23020 24073 \(-\) 34-1085/1086 6/6 HG970103.1:0-1086 efrB is a part of the EfrAB efflux pump and both efrA and efrB are necessary to confer multidrug resistance.
Sample8 emeA acridine_dye 97.72 97.12 16 23659 24813 \(-\) 1-1182/1182 1/27 AB091338:173-1355 A multidrug efflux pump from Enterococcus faecalis. There exist efflux activity of several antimicrobial agents such as DAPI Hoechst 33342 and acriflavine. Efflux of DAPI via EmeA was strongly inhibited by reserpine.
Sample8 lsaA lincosamide;macrolide;oxazolidinone;phenicol;pleuromutilin;streptogramin;tetracycline 100.00 97.86 8 35866 37362 \(-\) 1-1497/1497 0/0 AY225127.1:40-1537 LsaA is an ABC-F subfamily protein expressed in Enterococcus faecalis. It confers resistance to clindamycin quinupristin-dalfopristin and dalfopristin.


arg-annot

Sample1

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample1 (AGly)aphA6 NA 100.00 98.33 NODE_56_length_10210_cov_22.632192 8272 9051 \(+\) 1-780/780 0/0 JF949760:695-1474 (AGly)aphA6
Sample1 (AGly)armA NA 100.00 100.00 NODE_60_length_7576_cov_19.451527 6514 7287 \(-\) 1-774/774 0/0 AY220558:1978-2751 (AGly)armA
Sample1 (Bla)ampH NA 100.00 99.22 NODE_4_length_259554_cov_28.160970 34668 35828 \(-\) 1-1161/1161 0/0 CP003785:4208384-4209544 (Bla)ampH
Sample1 (Bla)blaKPC-3 NA 100.00 100.00 NODE_45_length_23679_cov_20.948606 14049 14930 \(+\) 1-882/882 0/0 JN255861:139-1020 (Bla)blaKPC-3
Sample1 (Bla)blaNDM-1 NA 100.00 100.00 NODE_84_length_3546_cov_28.774575 2466 3278 \(-\) 1-813/813 0/0 JQ080305:1-813 (Bla)blaNDM-1
Sample1 (Bla)blaOXA-9 NA 100.00 99.88 NODE_89_length_2852_cov_17.139459 229 1068 \(+\) 1-840/840 0/0 NC_015515:451-1290 (Bla)blaOXA-9
Sample1 (Bla)blaSHV-187 NA 100.00 99.54 NODE_85_length_3522_cov_41.898403 20 886 \(-\) 1-867/867 0/0 LN515533:1-867 (Bla)blaSHV-187
Sample1 (Bla)blaTEM-122 NA 100.00 99.77 NODE_89_length_2852_cov_17.139459 1768 2628 \(+\) 1-861/861 0/0 AY307100:1-861 (Bla)blaTEM-122
Sample1 (Fcyn)FosA6 NA 100.00 98.33 NODE_14_length_151513_cov_31.882346 135672 136091 \(-\) 1-420/420 0/0 KU254579:59422-59841 (Fcyn)FosA6
Sample1 (Flq)OqxA NA 100.00 99.15 NODE_17_length_122842_cov_28.181868 64068 65243 \(+\) 1-1176/1176 0/0 EU370913:46652-47827 (Flq)OqxA
Sample1 (Flq)OqxBgb NA 100.00 98.95 NODE_17_length_122842_cov_28.181868 65267 68419 \(+\) 1-3153/3153 0/0 EU370913:47851-51003 (Flq)OqxBgb
Sample1 (Flq)qnr-S1 NA 100.00 100.00 NODE_56_length_10210_cov_22.632192 3738 4394 \(+\) 1-657/657 0/0 AB187515:9737-10393 (Flq)qnr-S1
Sample1 (MLS)mph(A) NA 99.67 100.00 NODE_68_length_6118_cov_26.757987 147 1049 \(+\) 1-903/906 0/0 DQ445270:1626-2531 (MLS)mph(A)
Sample1 (MLS)mph(E) NA 100.00 99.89 NODE_60_length_7576_cov_19.451527 1800 2684 \(-\) 1-885/885 0/0 JF769133:8777-9661 (MLS)mph(E)
Sample1 (MLS)msr(E) NA 100.00 100.00 NODE_60_length_7576_cov_19.451527 2740 4215 \(-\) 1-1476/1476 0/0 JF769133:7246-8721 (MLS)msr(E)
Sample1 (Sul)sul1 NA 100.00 100.00 NODE_82_length_3659_cov_26.867113 2427 3266 \(+\) 1-840/840 0/0 AF071413:6700-7539 (Sul)sul1
Sample1 (Sul)sul2 NA 100.00 100.00 NODE_67_length_6209_cov_27.717221 3883 4698 \(-\) 1-816/816 0/0 EU360945:1617-2432 (Sul)sul2
Sample1 (Tmt)dfrA5 NA 100.00 100.00 NODE_82_length_3659_cov_26.867113 1429 1902 \(+\) 1-474/474 0/0 X12868:1306-1779 (Tmt)dfrA5


Sample2

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample2 (AGly)aadA1-pm NA 96.15 99.63 NODE_59_length_8503_cov_27.463684 1261 2059 \(+\) 30-831/831 1/3 JQ690540:7968-8798 (AGly)aadA1-pm
Sample2 (AGly)aadB NA 100.00 100.00 NODE_59_length_8503_cov_27.463684 680 1213 \(+\) 1-534/534 0/0 JQ690540:4275-4808 (AGly)aadB
Sample2 (AGly)armA NA 100.00 100.00 NODE_66_length_5980_cov_31.768592 273 1046 \(+\) 1-774/774 0/0 AY220558:1978-2751 (AGly)armA
Sample2 (Bla)ampH NA 100.00 99.14 NODE_1_length_492243_cov_27.186120 33962 35122 \(-\) 1-1161/1161 0/0 CP003785:4208384-4209544 (Bla)ampH
Sample2 (Bla)blaKPC-3 NA 100.00 100.00 NODE_48_length_21954_cov_52.979888 17158 18039 \(+\) 1-882/882 0/0 JN255861:139-1020 (Bla)blaKPC-3
Sample2 (Bla)blaSHV-106 NA 100.00 99.77 NODE_13_length_143880_cov_22.251622 115086 115946 \(+\) 1-861/861 0/0 AM941847:1-861 (Bla)blaSHV-106
Sample2 (Fcyn)FosA5 NA 100.00 96.19 NODE_25_length_81436_cov_30.505341 66696 67115 \(-\) 1-420/420 0/0 KP143090:1200-1619 (Fcyn)FosA5
Sample2 (Flq)OqxA NA 100.00 99.66 NODE_24_length_84154_cov_26.506904 53666 54841 \(-\) 1-1176/1176 0/0 EU370913:46652-47827 (Flq)OqxA
Sample2 (Flq)OqxBgb NA 100.00 98.83 NODE_24_length_84154_cov_26.506904 50490 53642 \(-\) 1-3153/3153 0/0 EU370913:47851-51003 (Flq)OqxBgb
Sample2 (MLS)mph(E) NA 100.00 99.89 NODE_66_length_5980_cov_31.768592 4876 5760 \(+\) 1-885/885 0/0 JF769133:8777-9661 (MLS)mph(E)
Sample2 (MLS)msr(E) NA 100.00 100.00 NODE_66_length_5980_cov_31.768592 3345 4820 \(+\) 1-1476/1476 0/0 JF769133:7246-8721 (MLS)msr(E)
Sample2 (Phe)catA1 NA 100.00 99.85 NODE_87_length_1659_cov_21.879267 300 959 \(+\) 1-660/660 0/0 V00622:244-903 (Phe)catA1
Sample2 (Sul)sul1 NA 100.00 100.00 NODE_59_length_8503_cov_27.463684 2564 3403 \(+\) 1-840/840 0/0 AF071413:6700-7539 (Sul)sul1


Sample3

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample3 (AGly)apH-Stph NA 100.00 99.38 NODE_4_length_124164_cov_55.531573 36344 37144 \(+\) 1-801/801 0/0 HE579073:1778413-1779213 (AGly)apH-Stph
Sample3 (Bla)blaI NA 95.54 98.35 NODE_89_length_3290_cov_522.302009 1 364 \(-\) 1-364/381 0/0 NG_047499:101-481 (Bla)blaI
Sample3 (Bla)blaR1_Bacilli NA 100.00 96.13 NODE_89_length_3290_cov_522.302009 354 2111 \(-\) 1-1758/1758 0/0 NG_047539:1-1758 (Bla)blaR1_Bacilli
Sample3 (Bla)blaZ NA 100.00 98.34 NODE_89_length_3290_cov_522.302009 2218 3063 \(+\) 1-846/846 0/0 AB245469:2235-3080 (Bla)blaZ
Sample3 (Flq)norA NA 99.91 91.25 NODE_5_length_123125_cov_66.683578 14544 15709 \(+\) 1-1166/1167 0/0 D90119:478-1644 (Flq)norA
Sample3 (Flq)norA NA 99.91 91.25 NODE_5_length_123125_cov_66.683578 107417 108582 \(-\) 1-1166/1167 0/0 D90119:478-1644 (Flq)norA
Sample3 (Phe)dha1 NA 100.00 98.48 NODE_6_length_102568_cov_74.986460 25025 26212 \(+\) 1-1188/1188 0/0 BA000018:2517801-2518988 (Phe)dha1
Sample3 (Tet)tet(38) NA 100.00 98.82 NODE_87_length_3816_cov_82.890189 571 1923 \(-\) 1-1353/1353 0/0 AY825285:1-1353 (Tet)tet(38)


Sample5

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample5 (Bla)Penicillin_Binding_Protein_Ecoli NA 100 91.17 NODE_1_length_833323_cov_12.8744 468361 470262 \(+\) 1-1902/1902 0/0 CP002291:664439-666340 (Bla)Penicillin_Binding_Protein_Ecoli


Sample7

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample7 (MLS)lsa(A) NA 100 99.40 10 103585 105081 \(+\) 1-1497/1497 0/0 AY225127:41-1537 (MLS)lsa(A)
Sample7 (MLS)mph(D) NA 100 99.88 1 149564 150397 \(+\) 1-834/834 0/0 NC_017312:2291580-2292413 (MLS)mph(D)
Sample7 (Tmt)dfrE NA 100 97.58 1 436056 436550 \(-\) 1-495/495 0/0 NG_055770:101-595 (Tmt)dfrE


Sample8

Sample Gene Resistance Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Product
Sample8 (MLS)lsa(A) NA 100 97.86 8 35866 37362 \(-\) 1-1497/1497 0/0 AY225127:41-1537 (MLS)lsa(A)
Sample8 (MLS)mph(D) NA 100 99.76 1 278326 279159 \(-\) 1-834/834 0/0 NC_017312:2291580-2292413 (MLS)mph(D)
Sample8 (Tmt)dfrE NA 100 97.98 14 10353 10847 \(-\) 1-495/495 0/0 NG_055770:101-595 (Tmt)dfrE


Antimicrobial Resistance Heatmaps

AMRfinder plus

NCBI

Megares

ResFinder

CARD

arg-annot

Virulence Factors

VFDB

Sample1

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample1 fyuA (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.80 NODE_1_length_409520_cov_22.884123 29393 31414 \(-\) 1-2022/2022 0/0 NP_405467 NA
Sample1 irp1 (irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.82 NODE_1_length_409520_cov_22.884123 35023 44514 \(-\) 1-9492/9492 0/0 NP_405471 NA
Sample1 irp2 (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.85 NODE_1_length_409520_cov_22.884123 44602 50709 \(-\) 1-6108/6108 0/0 NP_405472 NA
Sample1 iucB (iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301] 100.00 93.04 NODE_42_length_31563_cov_23.613003 6943 7890 \(+\) 1-948/948 0/0 NP_709455 NA
Sample1 iucC (iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073] 99.89 90.53 NODE_42_length_31563_cov_23.613003 7890 9630 \(+\) 1-1743/1743 2/2 NP_755500 NA
Sample1 yagZ/ecpA (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] 99.32 90.24 NODE_4_length_259554_cov_28.160970 6000 6583 \(+\) 1-584/588 0/0 NP_286010 NA
Sample1 ybtA (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.79 NODE_1_length_409520_cov_22.884123 50900 51859 \(-\) 1-960/960 0/0 NP_405473 NA
Sample1 ybtE (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.94 NODE_1_length_409520_cov_22.884123 31545 33122 \(-\) 1-1578/1578 0/0 NP_405468 NA
Sample1 ybtP (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.83 NODE_1_length_409520_cov_22.884123 52026 53828 \(+\) 1-1803/1803 0/0 NP_405474 NA
Sample1 ybtQ (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.89 NODE_1_length_409520_cov_22.884123 53815 55617 \(+\) 1-1803/1803 0/0 NP_405475 NA
Sample1 ybtS (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.85 NODE_1_length_409520_cov_22.884123 56918 58222 \(+\) 1-1305/1305 0/0 NP_405477 NA
Sample1 ybtT (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.75 NODE_1_length_409520_cov_22.884123 33126 33929 \(-\) 1-804/804 0/0 NP_405469 NA
Sample1 ybtU (ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.91 NODE_1_length_409520_cov_22.884123 33926 35026 \(-\) 1-1101/1101 0/0 NP_405470 NA
Sample1 ybtX (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.92 NODE_1_length_409520_cov_22.884123 55610 56890 \(+\) 1-1281/1281 0/0 NP_405476 NA


Sample2

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample2 fyuA (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.90 NODE_18_length_118566_cov_22.645967 68286 70307 \(-\) 1-2022/2022 0/0 NP_405467 NA
Sample2 irp1 (irp1) yersiniabactin biosynthetic protein Irp1 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.87 NODE_18_length_118566_cov_22.645967 73916 83407 \(-\) 1-9492/9492 0/0 NP_405471 NA
Sample2 irp2 (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.80 NODE_18_length_118566_cov_22.645967 83495 89602 \(-\) 1-6108/6108 0/0 NP_405472 NA
Sample2 iucB (iucB) aerobactin synthesis protein IucB [Aerobactin (VF0123)] [Shigella flexneri 2a str. 301] 100.00 93.14 NODE_51_length_18440_cov_24.502042 6943 7890 \(+\) 1-948/948 0/0 NP_709455 NA
Sample2 iucC (iucC) aerobactin siderophore biosynthesis protein IucC [Aerobactin (VF0229)] [Escherichia coli CFT073] 99.89 90.53 NODE_51_length_18440_cov_24.502042 7890 9630 \(+\) 1-1743/1743 2/2 NP_755500 NA
Sample2 yagZ/ecpA (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933] 99.32 90.07 NODE_1_length_492243_cov_27.186120 5295 5878 \(+\) 1-584/588 0/0 NP_286010 NA
Sample2 ybtA (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.90 NODE_18_length_118566_cov_22.645967 89793 90752 \(-\) 1-960/960 0/0 NP_405473 NA
Sample2 ybtE (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.94 NODE_18_length_118566_cov_22.645967 70438 72015 \(-\) 1-1578/1578 0/0 NP_405468 NA
Sample2 ybtP (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.83 NODE_18_length_118566_cov_22.645967 90919 92721 \(+\) 1-1803/1803 0/0 NP_405474 NA
Sample2 ybtQ (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.94 NODE_18_length_118566_cov_22.645967 92708 94510 \(+\) 1-1803/1803 0/0 NP_405475 NA
Sample2 ybtS (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.92 NODE_18_length_118566_cov_22.645967 95811 97115 \(+\) 1-1305/1305 0/0 NP_405477 NA
Sample2 ybtT (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.25 NODE_18_length_118566_cov_22.645967 72019 72822 \(-\) 1-804/804 0/0 NP_405469 NA
Sample2 ybtU (ybtU) yersiniabactin biosynthetic protein YbtU [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 100.00 NODE_18_length_118566_cov_22.645967 72819 73919 \(-\) 1-1101/1101 0/0 NP_405470 NA
Sample2 ybtX (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92] 100.00 99.92 NODE_18_length_118566_cov_22.645967 94503 95783 \(+\) 1-1281/1281 0/0 NP_405476 NA


Sample3

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample3 adsA (adsA) Adenosine synthase A [AdsA (VF0422)] [Staphylococcus aureus subsp. aureus MW2] 99.22 96.16 NODE_29_length_32051_cov_87.623734 27722 30022 \(+\) 1-2319/2319 1/18 NP_644838 NA
Sample3 cap8A (cap8A) capsular polysaccharide synthesis enzyme [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.84 NODE_59_length_11308_cov_75.576557 106 622 \(-\) 1-516/516 1/1 NP_644939 NA
Sample3 cap8B (cap8B) capsular polysaccharide synthesis enzyme Cap8B [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.32 NODE_26_length_32524_cov_82.900305 15483 16169 \(-\) 1-687/687 0/0 NP_644940 NA
Sample3 cap8B (cap8B) capsular polysaccharide synthesis enzyme Cap8B [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.32 NODE_26_length_32524_cov_82.900305 16356 17042 \(+\) 1-687/687 0/0 NP_644940 NA
Sample3 cap8C (cap8C) capsular polysaccharide synthesis enzyme Cap8C [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.48 NODE_26_length_32524_cov_82.900305 14716 15480 \(-\) 1-765/765 0/0 NP_644941 NA
Sample3 cap8C (cap8C) capsular polysaccharide synthesis enzyme Cap8C [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.48 NODE_26_length_32524_cov_82.900305 17045 17809 \(+\) 1-765/765 0/0 NP_644941 NA
Sample3 cap8D (cap8D) capsular polysaccharide synthesis enzyme Cap8D [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.97 NODE_26_length_32524_cov_82.900305 12873 14696 \(-\) 1-1824/1824 0/0 NP_644942 NA
Sample3 cap8D (cap8D) capsular polysaccharide synthesis enzyme Cap8D [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.97 NODE_26_length_32524_cov_82.900305 17829 19652 \(+\) 1-1824/1824 0/0 NP_644942 NA
Sample3 cap8E (cap8E) capsular polysaccharide synthesis enzyme Cap8E [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.57 NODE_26_length_32524_cov_82.900305 11855 12883 \(-\) 1-1029/1029 0/0 NP_644943 NA
Sample3 cap8E (cap8E) capsular polysaccharide synthesis enzyme Cap8E [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.57 NODE_26_length_32524_cov_82.900305 19642 20670 \(+\) 1-1029/1029 0/0 NP_644943 NA
Sample3 cap8F (cap8F) capsular polysaccharide synthesis enzyme Cap8F [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.75 NODE_26_length_32524_cov_82.900305 10733 11842 \(-\) 1-1110/1110 0/0 NP_644944 NA
Sample3 cap8F (cap8F) capsular polysaccharide synthesis enzyme Cap8F [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.75 NODE_26_length_32524_cov_82.900305 20683 21792 \(+\) 1-1110/1110 0/0 NP_644944 NA
Sample3 cap8G (cap8G) capsular polysaccharide synthesis enzyme Cap8G [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.20 NODE_26_length_32524_cov_82.900305 9605 10729 \(-\) 1-1125/1125 0/0 NP_644945 NA
Sample3 cap8G (cap8G) capsular polysaccharide synthesis enzyme Cap8G [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.20 NODE_26_length_32524_cov_82.900305 21796 22920 \(+\) 1-1125/1125 0/0 NP_644945 NA
Sample3 cap8H (cap8H) capsular polysaccharide synthesis enzyme Cap8H [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.07 NODE_26_length_32524_cov_82.900305 8523 9602 \(-\) 1-1080/1080 0/0 NP_644946 NA
Sample3 cap8H (cap8H) capsular polysaccharide synthesis enzyme Cap8H [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.07 NODE_26_length_32524_cov_82.900305 22923 24002 \(+\) 1-1080/1080 0/0 NP_644946 NA
Sample3 cap8I (cap8I) capsular polysaccharide synthesis enzyme Cap8I [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.71 NODE_26_length_32524_cov_82.900305 7136 8530 \(-\) 1-1395/1395 0/0 NP_644947 NA
Sample3 cap8I (cap8I) capsular polysaccharide synthesis enzyme Cap8I [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.71 NODE_26_length_32524_cov_82.900305 23995 25389 \(+\) 1-1395/1395 0/0 NP_644947 NA
Sample3 cap8J (cap8J) capsular polysaccharide synthesis enzyme Cap8J [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.75 NODE_26_length_32524_cov_82.900305 6582 7139 \(-\) 1-558/558 0/0 NP_644948 NA
Sample3 cap8J (cap8J) capsular polysaccharide synthesis enzyme Cap8J [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.75 NODE_26_length_32524_cov_82.900305 25386 25943 \(+\) 1-558/558 0/0 NP_644948 NA
Sample3 cap8K (cap8K) capsular polysaccharide synthesis enzyme Cap8K [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 96.69 NODE_26_length_32524_cov_82.900305 5335 6573 \(-\) 1-1239/1239 0/0 NP_644949 NA
Sample3 cap8K (cap8K) capsular polysaccharide synthesis enzyme Cap8K [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 96.69 NODE_26_length_32524_cov_82.900305 25952 27190 \(+\) 1-1239/1239 0/0 NP_644949 NA
Sample3 cap8L (cap8L) capsular polysaccharide synthesis enzyme Cap8L [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.26 NODE_26_length_32524_cov_82.900305 4096 5301 \(-\) 1-1206/1206 0/0 NP_644950 NA
Sample3 cap8L (cap8L) capsular polysaccharide synthesis enzyme Cap8L [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.26 NODE_26_length_32524_cov_82.900305 27224 28429 \(+\) 1-1206/1206 0/0 NP_644950 NA
Sample3 cap8M (cap8M) capsular polysaccharide synthesis enzyme Cap8M [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.75 NODE_26_length_32524_cov_82.900305 3528 4085 \(-\) 1-558/558 0/0 NP_644951 NA
Sample3 cap8M (cap8M) capsular polysaccharide synthesis enzyme Cap8M [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.75 NODE_26_length_32524_cov_82.900305 28440 28997 \(+\) 1-558/558 0/0 NP_644951 NA
Sample3 cap8N (cap8N) capsular polysaccharide synthesis enzyme Cap8N [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.64 NODE_26_length_32524_cov_82.900305 2641 3528 \(-\) 1-888/888 0/0 NP_644952 NA
Sample3 cap8N (cap8N) capsular polysaccharide synthesis enzyme Cap8N [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.64 NODE_26_length_32524_cov_82.900305 28997 29884 \(+\) 1-888/888 0/0 NP_644952 NA
Sample3 cap8O (cap8O) capsular polysaccharide synthesis enzyme Cap8O [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.89 NODE_26_length_32524_cov_82.900305 1324 2586 \(-\) 1-1263/1263 0/0 NP_644953 NA
Sample3 cap8O (cap8O) capsular polysaccharide synthesis enzyme Cap8O [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.89 NODE_26_length_32524_cov_82.900305 29939 31201 \(+\) 1-1263/1263 0/0 NP_644953 NA
Sample3 cap8P (cap8P) capsular polysaccharide synthesis enzyme Cap8P [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.87 NODE_26_length_32524_cov_82.900305 102 1247 \(-\) 1-1146/1146 0/0 NP_644954 NA
Sample3 cap8P (cap8P) capsular polysaccharide synthesis enzyme Cap8P [Capsule (VF0003)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.87 NODE_26_length_32524_cov_82.900305 31278 32423 \(+\) 1-1146/1146 0/0 NP_644954 NA
Sample3 chp (chp) chemotaxis-inhibiting protein CHIPS [CHIPS (VF0424)] [Staphylococcus aureus subsp. aureus str. Newman] 92.89 100.00 NODE_109_length_960_cov_266.593370 1 418 \(+\) 33-450/450 0/0 YP_001332911 NA
Sample3 chp (chp) chemotaxis-inhibiting protein CHIPS [CHIPS (VF0424)] [Staphylococcus aureus subsp. aureus str. Newman] 92.89 100.00 NODE_109_length_960_cov_266.593370 543 960 \(-\) 33-450/450 0/0 YP_001332911 NA
Sample3 ebp (ebp) cell surface elastin binding protein [EbpS (VF0008)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.40 NODE_2_length_257385_cov_46.985552 177325 178788 \(+\) 1-1461/1461 1/3 NP_646186 NA
Sample3 esaA (esaA) type VII secretion system protein EsaA [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.78 NODE_37_length_26881_cov_73.171885 12239 15268 \(-\) 1-3030/3030 0/0 NP_645074 NA
Sample3 esaB (esaB) type VII secretion system protein EsaB [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 100.00 NODE_37_length_26881_cov_73.171885 11567 11809 \(-\) 1-243/243 0/0 NP_645076 NA
Sample3 esaC (esaC) type VII secretion system protein secreted protein EsxC [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.47 NODE_37_length_26881_cov_73.171885 5337 5729 \(-\) 1-393/393 0/0 NP_645081 NA
Sample3 essA (essA) type VII secretion system protein EssA monotopic membrane protein [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 100.00 NODE_37_length_26881_cov_73.171885 11781 12239 \(-\) 1-459/459 0/0 NP_645075 NA
Sample3 essB (essB) type VII secretion system protein EssB monotopic membrane protein [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.40 NODE_37_length_26881_cov_73.171885 10220 11554 \(-\) 1-1335/1335 0/0 NP_645078 NA
Sample3 essC (essC) type VII secretion system protein EssC FtsK/SpoIIIE family ATPase [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.69 NODE_37_length_26881_cov_73.171885 5759 10198 \(-\) 1-4440/4440 0/0 NP_645079 NA
Sample3 esxA (esxA) type VII secretion system protein secreted protein EsxA [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.66 NODE_37_length_26881_cov_73.171885 15351 15644 \(-\) 1-294/294 0/0 NP_645073 NA
Sample3 esxB (esxB) type VII secretion system protein secreted protein EsxB [Type VII secretion system (VF0403)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.36 NODE_37_length_26881_cov_73.171885 5007 5321 \(-\) 1-315/315 0/0 NP_645082 NA
Sample3 fnbA (fnbA) fibronectin-binding protein A [FnBPs (VF0010)] [Staphylococcus aureus subsp. aureus MW2] 91.54 96.28 NODE_38_length_26410_cov_78.335913 23617 26410 \(+\) 1-2794/3048 3/8 NP_647238 NA
Sample3 geh (geh) glycerol ester hydrolase [Lipase (VF0012)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.30 NODE_7_length_75822_cov_72.897277 19999 22074 \(+\) 1-2073/2073 1/3 NP_645114 NA
Sample3 hld (hld) delta-hemolysin [<delta>-hemolysin (VF0007)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.26 NODE_8_length_72322_cov_70.965074 32254 32388 \(+\) 1-135/135 0/0 NP_646776 NA
Sample3 hld (hld) delta-hemolysin [<delta>-hemolysin (VF0007)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.26 NODE_8_length_72322_cov_70.965074 39935 40069 \(-\) 1-135/135 0/0 NP_646776 NA
Sample3 hlgA (hlgA) gamma-hemolysin chain II precursor [<gamma>-hemolysin (VF0011)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.36 NODE_6_length_102568_cov_74.986460 65302 66231 \(-\) 1-930/930 0/0 NP_647159 NA
Sample3 hlgB (hlgB) gamma-hemolysin component B [<gamma>-hemolysin (VF0011)] [Staphylococcus aureus subsp. aureus MW2] 100.00 93.05 NODE_6_length_102568_cov_74.986460 62808 63785 \(-\) 1-978/978 0/0 NP_647161 NA
Sample3 hlgC (hlgC) gamma-hemolysin component C [<gamma>-hemolysin (VF0011)] [Staphylococcus aureus subsp. aureus MW2] 100.00 92.83 NODE_6_length_102568_cov_74.986460 63787 64734 \(-\) 1-948/948 0/0 NP_647160 NA
Sample3 hly/hla (hly/hla) Alpha-Hemolysin precursor [<alpha>-hemolysin (VF0001)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.79 NODE_81_length_4934_cov_71.237549 1030 1989 \(+\) 1-960/960 0/0 NP_645861 NA
Sample3 hysA (hysA) hyaluronate lyase precursor [Hyaluronate lyase (VF0013)] [Staphylococcus aureus subsp. aureus MW2] 98.37 90.01 NODE_20_length_42470_cov_69.001061 9239 11650 \(-\) 1-2418/2448 7/14 NP_646946 NA
Sample3 icaA (icaA) N-acetylglucosaminyltransferase involved in polysaccharide intercellular adhesin(PIA) synthesis [Intercellular adhesion proteins (VF0014)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.11 NODE_56_length_12340_cov_94.944078 2419 3657 \(-\) 1-1239/1239 0/0 NP_647403 NA
Sample3 icaB (icaB) N-deacetylase involved in polysaccharide intercellular adhesin(PIA) synthesis [Intercellular adhesion proteins (VF0014)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.31 NODE_56_length_12340_cov_94.944078 1281 2153 \(-\) 1-873/873 0/0 NP_647405 NA
Sample3 icaC (icaC) intercellular adhesion protein C involved in polysaccharide intercellular adhesin(PIA) synthesis [Intercellular adhesion proteins (VF0014)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.05 NODE_56_length_12340_cov_94.944078 242 1294 \(-\) 1-1053/1053 0/0 NP_647406 NA
Sample3 icaD (icaD) intercellular adhesion protein D involved in polysaccharide intercellular adhesin(PIA) synthesis [Intercellular adhesion proteins (VF0014)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.35 NODE_56_length_12340_cov_94.944078 2150 2455 \(-\) 1-306/306 0/0 NP_647404 NA
Sample3 icaR (icaR) ica operon transcriptional regulator IcaR [Intercellular adhesion proteins (VF0014)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.75 NODE_56_length_12340_cov_94.944078 3821 4381 \(+\) 1-561/561 0/0 NP_647402 NA
Sample3 isdA (isdA) iron-regulated surface determinant protein A [Isd (VF0015)] [Staphylococcus aureus subsp. aureus str. Newman] 100.00 95.82 NODE_31_length_31121_cov_55.365287 27751 28803 \(+\) 1-1053/1053 0/0 YP_001332075 NA
Sample3 isdB (isdB) iron-regulated surface determinant protein B haemoglobin receptor [Isd (VF0015)] [Staphylococcus aureus subsp. aureus str. Newman] 99.85 95.82 NODE_31_length_31121_cov_55.365287 29006 30940 \(+\) 1-1938/1938 1/3 YP_001332074 NA
Sample3 isdC (isdC) iron-regulated surface determinant protein C [Isd (VF0015)] [Staphylococcus aureus subsp. aureus str. Newman] 99.85 96.49 NODE_31_length_31121_cov_55.365287 26859 27541 \(-\) 2-684/684 0/0 YP_001332076 NA
Sample3 isdD (isdD) iron-regulated surface determinant protein D [Isd (VF0015)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.24 NODE_31_length_31121_cov_55.365287 25783 26859 \(-\) 1-1077/1077 0/0 NP_645831 NA
Sample3 isdE (isdE) iron-regulated surface determinant protein E [Isd (VF0015)] [Staphylococcus aureus subsp. aureus str. Newman] 100.00 99.43 NODE_31_length_31121_cov_55.365287 24908 25786 \(-\) 1-879/879 0/0 YP_001332078 NA
Sample3 isdF (isdF) iron-regulated surface determinant protein F ATP-binding-cassette-type transmembrane transporter [Isd (VF0015)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.45 NODE_31_length_31121_cov_55.365287 23930 24895 \(-\) 1-966/966 0/0 NP_645833 NA
Sample3 isdG (isdG) iron-regulated surface determinant protein G [Isd (VF0015)] [Staphylococcus aureus subsp. aureus str. Newman] 100.00 98.46 NODE_31_length_31121_cov_55.365287 22792 23115 \(-\) 1-324/324 0/0 YP_001332081 NA
Sample3 lip (lip) triacylglycerol lipase precursor [Lipase (CVF091)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.26 NODE_55_length_12687_cov_88.535703 10465 12510 \(+\) 1-2046/2046 0/0 NP_647407 NA
Sample3 sak (sak) Staphylokinase precursor [Staphylokinase (VF0021)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.39 NODE_48_length_18462_cov_162.282990 16961 17452 \(+\) 1-492/492 0/0 NP_646702 NA
Sample3 sbi (sbi) IgG-binding protein SBI [Sbi (VF0423)] [Staphylococcus aureus subsp. aureus MW2] 100.00 93.53 NODE_6_length_102568_cov_74.986460 66767 68080 \(-\) 1-1314/1314 0/0 NP_647158 NA
Sample3 scn (scn) complement inhibitor SCIN [SCIN (VF0425)] [Staphylococcus aureus subsp. aureus str. Newman] 100.00 100.00 NODE_98_length_2325_cov_187.610573 772 1122 \(+\) 1-351/351 0/0 YP_001332910 NA
Sample3 sdrE (sdrE) Ser-Asp rich fibrinogen-binding bone sialoprotein-binding protein [SDr (VF0019)] [Staphylococcus aureus subsp. aureus MW2] 100.00 94.66 NODE_12_length_51989_cov_65.169696 5155 8616 \(+\) 1-3426/3426 2/36 NP_645335 NA
Sample3 sec (sec) staphylococcal enterotoxin C precursor [Enterotoxin C (CVF057)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.62 NODE_32_length_30161_cov_64.399488 5180 5980 \(+\) 1-801/801 0/0 NP_645576 NA
Sample3 sell (sell) staphylococcal enterotoxin L precursor [Enterotoxin-like L (CVF065)] [Staphylococcus aureus subsp. aureus MW2] 100.00 99.45 NODE_32_length_30161_cov_64.399488 6147 6869 \(-\) 1-723/723 0/0 NP_645577 NA
Sample3 srtB (srtB) NPQTN specific sortase B [Isd (VF0015)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.64 NODE_31_length_31121_cov_55.365287 23134 23868 \(-\) 1-735/735 0/0 NP_645834 NA
Sample3 sspA (sspA) serine protease; V8 protease; glutamyl endopeptidase [V8 protease (VF0023)] [Staphylococcus aureus subsp. aureus MW2] 100.00 93.91 NODE_1_length_266693_cov_59.525169 115889 116890 \(-\) 1-984/984 2/18 NP_645749 NA
Sample3 sspA (sspA) serine protease; V8 protease; glutamyl endopeptidase [V8 protease (VF0023)] [Staphylococcus aureus subsp. aureus MW2] 100.00 93.91 NODE_1_length_266693_cov_59.525169 149804 150805 \(+\) 1-984/984 2/18 NP_645749 NA
Sample3 sspB (sspB) staphopain cysteine proteinase SspB [Staphopain (VF0006)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.55 NODE_1_length_266693_cov_59.525169 114626 115807 \(-\) 1-1182/1182 0/0 NP_645748 NA
Sample3 sspB (sspB) staphopain cysteine proteinase SspB [Staphopain (VF0006)] [Staphylococcus aureus subsp. aureus MW2] 100.00 97.55 NODE_1_length_266693_cov_59.525169 150887 152068 \(+\) 1-1182/1182 0/0 NP_645748 NA
Sample3 sspC (sspC) Staphostatin B [Staphopain (VF0006)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.79 NODE_1_length_266693_cov_59.525169 114259 114588 \(-\) 1-330/330 0/0 NP_645747 NA
Sample3 sspC (sspC) Staphostatin B [Staphopain (VF0006)] [Staphylococcus aureus subsp. aureus MW2] 100.00 98.79 NODE_1_length_266693_cov_59.525169 152106 152435 \(+\) 1-330/330 0/0 NP_645747 NA


Sample4

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample4 cpa (cpa) fibronectin-binding protein GAS pilus tip adhesin [pilus (VF0531)] [Streptococcus pyogenes MGAS5005] 100.00 100.00 6 31774 34062 \(+\) 1-2289/2289 0/0 YP_281471 NA
Sample4 emm (emm) M protein type 1 [M protein (VF0242)] [Streptococcus pyogenes M1 GAS] 100.00 99.86 3 8218 9672 \(-\) 1-1455/1455 0/0 NP_269973 NA
Sample4 fbp54 (fbp54) fibronectin-bing protein Fbp54 [FBPs (VF0243)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 1 264765 266417 \(+\) 1-1653/1653 0/0 NP_269190 NA
Sample4 fctA (fctA) major pilin FctA [pilus (VF0531)] [Streptococcus pyogenes MGAS5005] 100.00 100.00 6 34645 35667 \(+\) 1-1023/1023 0/0 YP_281473 NA
Sample4 fctB (fctB) minor pilin FctB [pilus (VF0531)] [Streptococcus pyogenes MGAS5005] 100.00 100.00 6 36412 37059 \(+\) 1-648/648 0/0 YP_281475 NA
Sample4 grab (grab) protein GRAB (protein G-related alpha 2M-binding protein) [GRAB (VF0254)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 5 86640 87293 \(+\) 1-654/654 0/0 NP_269464 NA
Sample4 hasA (hasA) hyaluronate synthase [Hyaluronic acid capsule (VF0244)] [Streptococcus pyogenes M1 GAS] 100.00 99.84 10 35379 36638 \(-\) 1-1260/1260 0/0 NP_270107 NA
Sample4 hasB (hasB) UDP-glucose 6-dehydrogenase [Hyaluronic acid capsule (VF0244)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 10 34135 35343 \(-\) 1-1209/1209 0/0 NP_270108 NA
Sample4 hasC (hasC) UDP-glucose pyrophosphorylase [Hyaluronic acid capsule (VF0244)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 10 33039 33953 \(-\) 1-915/915 0/0 NP_270109 NA
Sample4 ideS/mac (ideS/mac) immunoglobulin G-degrading enzyme [IdeS (VF0284)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 1 336429 337448 \(+\) 1-1020/1020 0/0 NP_269065 NA
Sample4 lepA (lepA) signal peptidase I [pilus (VF0531)] [Streptococcus pyogenes MGAS5005] 100.00 100.00 6 34055 34612 \(+\) 1-558/558 0/0 YP_281472 NA
Sample4 lmb (lmb) laminin-binding surface protein [Lmb (VF0275)] [Streptococcus agalactiae 2603V/R] 100.00 98.37 7 91 1011 \(+\) 1-921/921 0/0 NP_688239 NA
Sample4 mf/spd (mf/spd) deoxyribonuclease [DNase (VF0252)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 3 26287 27102 \(-\) 1-816/816 0/0 NP_269989 NA
Sample4 mf3 (mf3) deoxyribonuclease [DNase (VF0252)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 5 19643 20449 \(-\) 1-807/807 0/0 NP_269520 NA
Sample4 scpA (scpA) C5a peptidase precursor [C5a peptidase (VF0245)] [Streptococcus pyogenes M1 GAS] 98.56 98.56 3 1352 4846 \(-\) 1-3546/3546 1/51 NP_269970 NA
Sample4 sic (sic) inhibitor of complement-mediated lysis [SIC (VF0255)] [Streptococcus pyogenes M1 GAS] 98.71 93.15 3 7064 8029 \(-\) 1-927/927 3/63 NP_269972 NA
Sample4 ska (ska) streptokinase A precursor [Streptokinase (VF0247)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 7 26965 28287 \(-\) 1-1323/1323 0/0 NP_269944 NA
Sample4 slo (slo) streptolysin O precursor [SLO (VF0250)] [Streptococcus pyogenes M1 GAS] 100.00 98.78 6 66471 68186 \(+\) 1-1716/1716 0/0 NP_268546 NA
Sample4 smeZ (smeZ) streptococcal mitogenic exotoxin Z [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 7 9641 10342 \(-\) 1-702/702 0/0 NP_269959 NA
Sample4 spea (spea) streptococcal exotoxin A precursor - phage associated [Spes (VF0248)] [Streptococcus pyogenes MGAS315] 100.00 99.73 1 24132 24887 \(-\) 1-756/756 0/0 NP_665105 NA
Sample4 speB (speB) pyrogenic exotoxin B [SpeB (VF0249)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 3 23068 24264 \(-\) 1-1197/1197 0/0 NP_269985 NA
Sample4 speg (speg) streptococcal exotoxin G precursor [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 14 4124 4828 \(-\) 1-705/705 0/0 NP_268582 NA
Sample4 spej (spej) streptococcal exotoxin J precursor [Spes (VF0248)] [Streptococcus pyogenes M1 GAS] 100.00 100.00 1 645158 645856 \(+\) 1-699/699 0/0 NP_268735 NA
Sample4 srtC1 (srtC1) sortase [pilus (VF0531)] [Streptococcus pyogenes MGAS5005] 100.00 100.00 6 35677 36390 \(+\) 1-714/714 0/0 YP_281474 NA


Sample5

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample5 cdtA (cdtA) cytolethal distending toxin A [CDT (VF0185)] [Escherichia coli O157:H str. 493/89] 100.00 90.61 NODE_4_length_290048_cov_13.1184 54090 54866 \(+\) 1-777/777 0/0 CAD48849 NA
Sample5 cdtB (cdtB) cytolethal distending toxin B [CDT (VF0185)] [Escherichia coli O157:H str. 493/89] 100.00 90.00 NODE_4_length_290048_cov_13.1184 54863 55672 \(+\) 1-810/810 0/0 CAD48850 NA
Sample5 cesAB (cesAB) chaperone for EspA and EspB [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 99.38 94.72 NODE_9_length_234966_cov_12.9153 23698 24019 \(+\) 3-324/324 0/0 NP_290286 NA
Sample5 cesD (cesD) chaperone for EspB and EspD [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 93.86 NODE_9_length_234966_cov_12.9153 29871 30326 \(-\) 1-456/456 0/0 NP_290276 NA
Sample5 cesD2 (cesD2) chaperone for EspD [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 99.75 96.56 NODE_9_length_234966_cov_12.9153 52227 52633 \(+\) 1-407/408 0/0 NP_290253 NA
Sample5 cesL (cesL) chaperone for SepL [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 91.53 NODE_9_length_234966_cov_12.9153 33861 34214 \(+\) 1-354/354 0/0 NP_290270 NA
Sample5 cesT (cesT) multieffector chaperone [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 95.12 NODE_9_length_234966_cov_12.9153 43412 43882 \(+\) 1-471/471 0/0 NP_290260 NA
Sample5 chuU (chuU) heme permease protein ChuU [Chu (VF0227)] [Escherichia coli CFT073] 100.00 91.24 NODE_8_length_237146_cov_13.3532 225040 226032 \(+\) 1-993/993 0/0 NP_756179 NA
Sample5 chuW (chuW) Putative oxygen independent coproporphyrinogen III oxidase [Chu (VF0227)] [Escherichia coli CFT073] 100.00 92.15 NODE_8_length_237146_cov_13.3532 222522 223859 \(+\) 1-1338/1338 0/0 NP_756176 NA
Sample5 entA (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 92.24 NODE_1_length_833323_cov_12.8744 505781 506527 \(-\) 1-747/747 0/0 NP_752614 NA
Sample5 entB (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 92.89 NODE_1_length_833323_cov_12.8744 506527 507384 \(-\) 1-858/858 0/0 NP_752613 NA
Sample5 entC (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 90.15 NODE_1_length_833323_cov_12.8744 509018 510205 \(-\) 1-1188/1188 0/0 NP_752611 NA
Sample5 entE (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 91.19 NODE_1_length_833323_cov_12.8744 507398 509008 \(-\) 1-1611/1611 0/0 NP_752612 NA
Sample5 entS (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073] 100.00 94.88 NODE_1_length_833323_cov_12.8744 511342 512592 \(-\) 1-1251/1251 0/0 NP_752609 NA
Sample5 escC (escC) Type III secretion system secretin EscC [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 91.49 NODE_9_length_234966_cov_12.9153 30340 31878 \(-\) 1-1539/1539 0/0 NP_290275 NA
Sample5 escD (escD) Type III secretion system outer MS ring protein EscD [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 95.09 NODE_9_length_234966_cov_12.9153 47046 48266 \(-\) 1-1221/1221 0/0 NP_290258 NA
Sample5 escE (escE) chaperone for EscF [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 94.52 NODE_9_length_234966_cov_12.9153 23474 23692 \(+\) 1-219/219 0/0 NP_290287 NA
Sample5 escF (escF) Type III secretion system needle filament protein EscF [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 96.85 NODE_9_length_234966_cov_12.9153 52671 52892 \(+\) 1-222/222 0/0 NP_290252 NA
Sample5 escG (escG) chaperone for EscF [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 94.62 90.53 NODE_9_length_234966_cov_12.9153 52898 53161 \(+\) 1-264/279 0/0 NP_290251 NA
Sample5 escJ (escJ) Type III secretion system inner MS ring protein EscJ [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 90.92 NODE_9_length_234966_cov_12.9153 32339 32911 \(-\) 1-573/573 0/0 NP_290273 NA
Sample5 escL (escL) negative regulator EscL stator protein [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 93.17 NODE_9_length_234966_cov_12.9153 24641 25255 \(+\) 1-615/615 0/0 NP_290284 NA
Sample5 escN (escN) ATPase EscN [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 94.18 NODE_9_length_234966_cov_12.9153 36222 37562 \(+\) 1-1341/1341 0/0 NP_290268 NA
Sample5 escO (escO) positive regulator EscO [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 95.77 NODE_9_length_234966_cov_12.9153 37565 37942 \(+\) 1-378/378 0/0 NP_290267 NA
Sample5 escR (escR) Type III secretion systemminor export apparatus protein EscR [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 97.25 NODE_9_length_234966_cov_12.9153 25260 25913 \(+\) 1-654/654 0/0 NP_290283 NA
Sample5 escS (escS) Type III secretion systemminor export apparatus protein EscS [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 96.67 NODE_9_length_234966_cov_12.9153 25913 26182 \(+\) 1-270/270 0/0 NP_290282 NA
Sample5 escT (escT) Type III secretion system minor export apparatus protein EscT [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 94.72 NODE_9_length_234966_cov_12.9153 26182 26958 \(+\) 1-777/777 0/0 NP_290281 NA
Sample5 escU (escU) Type III secretion system export apparatus switch protein EscU [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 96.24 NODE_9_length_234966_cov_12.9153 26951 27988 \(+\) 1-1038/1038 0/0 NP_290280 NA
Sample5 escV (escV) Type III secretion system major export apparatus protein [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 94.72 NODE_9_length_234966_cov_12.9153 34211 36238 \(+\) 1-2028/2028 0/0 NP_290269 NA
Sample5 espG (espG) Type III secretion system effector EspG GTPase activating protein [EspG (VF0201)] [Escherichia coli O157:H7 str. EDL933] 100.00 90.14 NODE_9_length_234966_cov_12.9153 20737 21933 \(-\) 1-1197/1197 0/0 NP_290289 NA
Sample5 espM2 (espM2) Type III secretion system effector EspM2 Rho guanine exchange factor [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 97.12 NODE_5_length_284821_cov_12.9843 280887 281477 \(-\) 1-591/591 0/0 NP_289175 NA
Sample5 espW (espW) Type III secretion system effector EspW [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 95.75 NODE_5_length_284821_cov_12.9843 282388 283446 \(+\) 1-1059/1059 0/0 NP_289177 NA
Sample5 etgA (etgA) T3SS-associated peptidoglycan lytic enzyme [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 94.12 NODE_9_length_234966_cov_12.9153 27985 28443 \(-\) 1-459/459 0/0 NP_290279 NA
Sample5 fepA (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 90.76 NODE_1_length_833323_cov_12.8744 522403 524652 \(+\) 1-2241/2241 1/9 NP_752600 NA
Sample5 fepB (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 91.64 NODE_1_length_833323_cov_12.8744 510382 511338 \(+\) 1-957/957 0/0 NP_752610 NA
Sample5 fepC (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 93.63 NODE_1_length_833323_cov_12.8744 514693 515508 \(+\) 1-816/816 0/0 NP_752606 NA
Sample5 fepD (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 92.23 NODE_1_length_833323_cov_12.8744 512691 513707 \(+\) 1-1017/1017 0/0 NP_752608 NA
Sample5 fepG (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073] 100.00 92.35 NODE_1_length_833323_cov_12.8744 513704 514696 \(+\) 1-993/993 0/0 NP_752607 NA
Sample5 fes (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073] 100.00 90.61 NODE_1_length_833323_cov_12.8744 520960 522162 \(-\) 1-1203/1203 0/0 NP_752602 NA
Sample5 gspC (gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 90.25 NODE_2_length_652771_cov_13.1584 328380 329210 \(+\) 1-831/831 0/0 YP_404599 NA
Sample5 gspD (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 91.84 NODE_2_length_652771_cov_13.1584 329450 331300 \(+\) 1-1836/1836 1/15 YP_404600 NA
Sample5 gspE (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 93.17 NODE_2_length_652771_cov_13.1584 331300 332793 \(+\) 1-1494/1494 0/0 YP_404601 NA
Sample5 gspF (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 92.17 NODE_2_length_652771_cov_13.1584 332793 333992 \(+\) 1-1200/1200 0/0 YP_404602 NA
Sample5 gspG (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 92.54 NODE_2_length_652771_cov_13.1584 334033 334488 \(+\) 1-456/456 0/0 YP_404603 NA
Sample5 gspJ (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 90.88 NODE_2_length_652771_cov_13.1584 335456 336025 \(+\) 1-570/570 0/0 YP_404606 NA
Sample5 gspK (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197] 100.00 90.90 NODE_2_length_652771_cov_13.1584 336022 336999 \(+\) 1-978/978 0/0 YP_404607 NA
Sample5 nleE (nleE) Type III secretion system effector NleE [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933] 100.00 90.96 NODE_9_length_234966_cov_12.9153 222560 223234 \(+\) 1-675/675 0/0 NP_289554 NA
Sample5 ompA (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218] 100.00 94.21 NODE_1_length_833323_cov_12.8744 75770 76822 \(+\) 1-1041/1041 1/12 AAF37887 NA
Sample5 sepL (sepL) Type III secretion system secretion gatekeeper SepL [TTSS (VF0191)] [Escherichia coli O157:H7 str. EDL933] 100.00 92.05 NODE_9_length_234966_cov_12.9153 48409 49464 \(+\) 1-1056/1056 0/0 NP_290257 NA
Sample5 shuA (shuA) outer membrane heme/hemoglobin receptor ShuA [Shu (VF0256)] [Shigella dysenteriae Sd197] 100.00 90.07 NODE_8_length_237146_cov_13.3532 218913 220895 \(-\) 1-1983/1983 0/0 YP_405019 NA


Sample7

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample7 ace (ace) collagen adhesin protein [Ace (VF0355)] [Enterococcus faecalis V583] 100.00 96.99 4 46753 48777 \(+\) 1-2025/2025 0/0 NP_814829 NA
Sample7 bopD (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583] 100.00 99.11 5 79591 80601 \(+\) 1-1011/1011 0/0 NP_814691 NA
Sample7 cpsA (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.63 9 801 1616 \(-\) 1-816/816 0/0 NP_816141 NA
Sample7 cpsB (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.50 9 4 804 \(-\) 1-801/801 0/0 NP_816140 NA
Sample7 ebpA (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.49 4 33894 37205 \(+\) 1-3312/3312 0/0 NP_814821 NA
Sample7 ebpB (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.37 4 37209 38639 \(+\) 1-1431/1431 0/0 NP_814822 NA
Sample7 ebpC (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.05 4 38636 40519 \(+\) 1-1878/1878 1/6 NP_814823 NA
Sample7 EF0818 (EF0818) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583] 100.00 99.20 3 14836 17850 \(-\) 1-3015/3015 0/0 NP_814561 NA
Sample7 EF3023 (EF3023) polysaccharide lyase family 8 [Hyaluronidase (VF0359)] [Enterococcus faecalis V583] 100.00 98.54 12 21908 26026 \(-\) 1-4119/4119 0/0 NP_816637 NA
Sample7 efaA (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583] 100.00 99.89 1 41749 42675 \(-\) 1-927/927 0/0 NP_815739 NA
Sample7 fss1 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583] 100.00 98.86 8 120517 126480 \(-\) 1-5964/5964 0/0 NP_813892 NA
Sample7 gelE (gelE) coccolysin [Gelatinase (VF0357)] [Enterococcus faecalis V583] 100.00 98.89 1 201365 202898 \(+\) 1-1533/1533 1/1 NP_815516 NA
Sample7 prgB/asc10 (prgB/asc10) aggregation substance PrgB/Asc10 [AS (VF0352)] [Enterococcus faecalis V583] 99.74 94.70 14 11075 14986 \(+\) 1-3918/3918 5/14 NP_817031 NA
Sample7 sprE (sprE) serine proteinase V8 family [SprE (VF0358)] [Enterococcus faecalis V583] 100.00 98.48 1 202947 203801 \(+\) 1-855/855 0/0 NP_815515 NA
Sample7 srtC (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.30 4 40613 41467 \(+\) 1-855/855 0/0 NP_814824 NA


Sample8

Sample Gene Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample8 bopD (bopD) sugar-binding transcriptional regulator LacI family [BopD (VF0362)] [Enterococcus faecalis V583] 100.00 99.21 7 116154 117164 \(-\) 1-1011/1011 0/0 NP_814691 NA
Sample8 cpsA (cpsA) undecaprenyl diphosphate synthase [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.51 1 656568 657383 \(-\) 1-816/816 0/0 NP_816141 NA
Sample8 cpsB (cpsB) phosphatidate cytidylyltransferase [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.62 1 655771 656571 \(-\) 1-801/801 0/0 NP_816140 NA
Sample8 cpsC (cpsC) teichoic acid biosynthesis protein putative [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.40 1 654129 655298 \(-\) 1-1170/1170 0/0 NP_816139 NA
Sample8 cpsD (cpsD) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.05 1 652644 654110 \(-\) 1-1467/1467 0/0 NP_816138 NA
Sample8 cpsE (cpsE) glycosyl transferase group 2 family protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.36 1 650064 652574 \(-\) 1-2511/2511 0/0 NP_816137 NA
Sample8 cpsF (cpsF) CpsF protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.53 1 649189 650040 \(-\) 1-852/852 0/0 NP_816136 NA
Sample8 cpsG (cpsG) MurB family protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.67 1 646709 649162 \(-\) 1-2454/2454 0/0 NP_816135 NA
Sample8 cpsH (cpsH) lipoprotein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.50 1 646293 646691 \(-\) 1-399/399 0/0 NP_816134 NA
Sample8 cpsI (cpsI) UDP-galactopyranose mutase [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.56 1 645095 646234 \(-\) 1-1140/1140 0/0 NP_816133 NA
Sample8 cpsJ (cpsJ) ABC transporter ATP-binding protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 99.55 1 643726 645069 \(-\) 1-1344/1344 0/0 NP_816132 NA
Sample8 cpsK (cpsK) ABC transporter permease protein [Capsule (VF0361)] [Enterococcus faecalis V583] 100.00 98.40 1 642914 643726 \(-\) 1-813/813 0/0 NP_816131 NA
Sample8 ebpA (ebpA) endocarditis and biofilm-associated pilus tip protein EbpA [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.55 16 13027 16338 \(-\) 1-3312/3312 0/0 NP_814821 NA
Sample8 ebpB (ebpB) endocarditis and biofilm-associated pilus minor subunit EbpB [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 99.23 16 11593 13023 \(-\) 1-1431/1431 0/0 NP_814822 NA
Sample8 ebpC (ebpC) endocarditis and biofilm-associated pilus major subunit EbpC [Ebp pili (VF0538)] [Enterococcus faecalis V583] 100.00 98.99 16 9713 11596 \(-\) 1-1878/1878 1/6 NP_814823 NA
Sample8 efaA (efaA) endocarditis specific antigen [EfaA (VF0354)] [Enterococcus faecalis V583] 100.00 99.68 1 386430 387356 \(+\) 1-927/927 0/0 NP_815739 NA
Sample8 fss1 (fss1) Enterococcus faecalis surface protein Fss1 fibrinogen binding protein [Fibrinogen binding protein (AI271)] [Enterococcus faecalis V583] 100.00 98.46 3 116629 122592 \(-\) 1-5964/5964 0/0 NP_813892 NA
Sample8 srtC (srtC) sortase [Ebp pili (VF0538)] [Enterococcus faecalis V583] 98.83 99.41 16 8775 9619 \(-\) 1-845/855 0/0 NP_814824 NA


Virulencefinder

Sample1

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample1 ccI 100.00 1686 / 1686 Cloacin DQ298019 virulence_ecoli NODE_57_length_9371_cov_180.047773 6559..8244
Sample1 clpK1 99.07 2786 / 2883 heat shock survival AAA family ATPase ClpK. thermal stress survival WP_053271808 virulence_ecoli NODE_65_length_6396_cov_25.027694 2381..5166
Sample1 fimH 100.00 489 / 489 Type 1 fimbriae NA virulence_ecoli NODE_26_length_87806_cov_31.164963 13225..13713
Sample1 fyuA 99.85 2022 / 2022 Siderophore receptor CAY233333 virulence_ecoli NODE_1_length_409520_cov_22.884123 29393..31414
Sample1 irp2 99.79 6108 / 6108 High molecular weight protein 2 non-ribosomal peptide synthetase NZ_UEMD01000021 virulence_ecoli NODE_1_length_409520_cov_22.884123 44602..50709
Sample1 iucC 90.59 1743 / 1743 Aerobactin synthetase CYAZ01000069 virulence_ecoli NODE_42_length_31563_cov_23.613003 7890..9630
Sample1 iutA 99.45 2190 / 2190 Ferric aerobactin receptor FLXF01000001 virulence_ecoli NODE_32_length_73384_cov_22.478795 51490..53679
Sample1 iutA 99.65 1722 / 1722 Ferric aerobactin receptor UDFN01000030 virulence_ecoli NODE_42_length_31563_cov_23.613003 11466..13187
Sample1 mchF 100.00 2097 / 2097 ABC transporter protein MchF AF063590 virulence_ecoli NODE_2_length_385203_cov_24.836368 355682..357778
Sample1 mrkA 95.95 592 / 597 type 3 fimbrial major subunit ABW83989 virulence_ecoli NODE_26_length_87806_cov_31.164963 78..669
Sample1 traT 100.00 777 / 777 Outer membrane protein complement resistance KY798506 virulence_ecoli NODE_76_length_4392_cov_18.530939 3079..3855


Sample2

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample2 ccI 100.00 1686 / 1686 Cloacin DQ298019 virulence_ecoli NODE_57_length_9371_cov_158.965677 5981..7666
Sample2 fimH 99.39 489 / 489 Type 1 fimbriae NA virulence_ecoli NODE_7_length_223591_cov_30.580272 117476..117964
Sample2 fyuA 100.00 2022 / 2022 Siderophore receptor CU928163 virulence_ecoli NODE_18_length_118566_cov_22.645967 68286..70307
Sample2 irp2 100.00 6108 / 6108 High molecular weight protein 2 non-ribosomal peptide synthetase NZ_UEMU01000024 virulence_ecoli NODE_18_length_118566_cov_22.645967 83495..89602
Sample2 iucC 90.59 1743 / 1743 Aerobactin synthetase CYAZ01000069 virulence_ecoli NODE_51_length_18440_cov_24.502042 7890..9630
Sample2 iutA 99.41 2190 / 2190 Ferric aerobactin receptor FLWH01000001 virulence_ecoli NODE_8_length_202783_cov_22.745040 63671..65860
Sample2 iutA 99.65 1722 / 1722 Ferric aerobactin receptor UDFN01000030 virulence_ecoli NODE_51_length_18440_cov_24.502042 11466..13187
Sample2 mrkA 96.10 615 / 597 type 3 fimbrial major subunit ABW83989 virulence_ecoli NODE_7_length_223591_cov_30.580272 104304..104918
Sample2 nlpI 90.07 886 / 885 lipoprotein NlpI precursor CP000243 virulence_ecoli NODE_4_length_282012_cov_30.847958 183372..184256
Sample2 terC 99.33 1041 / 1041 Tellurium ion resistance protein UGAE01000003 virulence_ecoli NODE_33_length_50445_cov_22.742555 24174..25214


Sample3

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample3 aur 99.15 1530 / 1530 aureolysin CP003808.1 s.aureus_exoenzyme NODE_18_length_42988_cov_83.614353 32482..34011
Sample3 hlgA 100.00 930 / 930 gamma-hemolysin chain II precursor CP006044.1 s.aureus_toxin NODE_6_length_102568_cov_74.986460 65302..66231
Sample3 hlgB 100.00 977 / 977 gamma-hemolysin component B precursor CP012756.1 s.aureus_toxin NODE_6_length_102568_cov_74.986460 62809..63785
Sample3 hlgC 100.00 948 / 948 gamma-hemolysin component C CP006044.1 s.aureus_toxin NODE_6_length_102568_cov_74.986460 63787..64734
Sample3 sak 99.80 492 / 492 staphylokinase CP000253.1 s.aureus_hostimm NODE_48_length_18462_cov_162.282990 16961..17452
Sample3 sak 99.80 492 / 492 staphylokinase CP003979.1 s.aureus_hostimm NODE_48_length_18462_cov_162.282990 16961..17452
Sample3 sak 99.80 492 / 492 staphylokinase HE681097.1 s.aureus_hostimm NODE_48_length_18462_cov_162.282990 16961..17452
Sample3 scn 100.00 351 / 351 staphylococcal complement inhibitor AP009351.1 s.aureus_hostimm NODE_98_length_2325_cov_187.610573 772..1122
Sample3 sec 100.00 801 / 801 enterotoxin C AB860417.1 s.aureus_toxin NODE_32_length_30161_cov_64.399488 5180..5980
Sample3 sec3 100.00 801 / 801 M28364.1 s.aureus_toxin NODE_32_length_30161_cov_64.399488 5180..5980
Sample3 seg 99.87 777 / 777 enterotoxin G CP001844.2 s.aureus_toxin NODE_60_length_10708_cov_61.516662 1849..2625
Sample3 sei 99.59 729 / 729 enterotoxin I BA000018.3 s.aureus_toxin NODE_60_length_10708_cov_61.516662 4626..5354
Sample3 sei 99.59 729 / 729 enterotoxin I CP011147.1 s.aureus_toxin NODE_60_length_10708_cov_61.516662 4626..5354
Sample3 sel 99.45 723 / 723 enterotoxin L AF217235.1 s.aureus_toxin NODE_32_length_30161_cov_64.399488 6147..6869
Sample3 sel 99.45 723 / 723 enterotoxin L BA000018.3 s.aureus_toxin NODE_32_length_30161_cov_64.399488 6147..6869
Sample3 sem 99.58 720 / 720 enterotoxin M BA000018.3 s.aureus_toxin NODE_60_length_10708_cov_61.516662 5389..6108
Sample3 sen 100.00 777 / 777 enterotoxin N BA000018.3 s.aureus_toxin NODE_60_length_10708_cov_61.516662 2908..3684
Sample3 seo 100.00 783 / 783 enterotoxin O BA000018.3 s.aureus_toxin NODE_60_length_10708_cov_61.516662 6388..7170
Sample3 seu 99.74 771 / 771 enterotoxin U HE681097.1 s.aureus_toxin NODE_60_length_10708_cov_61.516662 3702..4472


Sample5

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample5 cdt-VIB 99.75 810 / 810 Cytolethal distending toxin VI sub unit B AB472834 virulence_ecoli NODE_4_length_290048_cov_13.1184 54863..55672
Sample5 chuA 99.80 1983 / 1983 Outer membrane hemin receptor CYCK01000002 virulence_ecoli NODE_8_length_237146_cov_13.3532 218913..220895
Sample5 cia 100.00 147 / 147 Colicin ia QMGM01000002 virulence_ecoli NODE_17_length_99884_cov_10.8751 23229..23375
Sample5 eae-g04-sigma 99.54 2808 / 2808 AJ781125 virulence_ecoli NODE_9_length_234966_cov_12.9153 43943..46750
Sample5 espA 97.58 579 / 579 Type III secretions system AJ303141 virulence_ecoli NODE_9_length_234966_cov_12.9153 49522..50100
Sample5 espA 97.58 579 / 579 Type III secretions system AY223511 virulence_ecoli NODE_9_length_234966_cov_12.9153 49522..50100
Sample5 espB 99.79 945 / 945 Secreted protein B AP010958 virulence_ecoli NODE_9_length_234966_cov_12.9153 51276..52220
Sample5 espF 93.11 624 / 624 EPEC secreted protein F; Type III secretion system AF116900 virulence_ecoli NODE_9_length_234966_cov_12.9153 53392..54015
Sample5 fimH 100.00 489 / 489 Type 1 fimbriae NA virulence_ecoli NODE_16_length_116703_cov_13.7971 6266..6754
Sample5 iss 90.44 293 / 294 Increased serum survival CP001855 virulence_ecoli NODE_5_length_284821_cov_12.9843 246803..247095
Sample5 nleB 92.32 990 / 990 Non-LEE encoded effector B FN543502 virulence_ecoli NODE_9_length_234966_cov_12.9153 221536..222525
Sample5 nlpI 98.53 885 / 885 lipoprotein NlpI precursor CP000243 virulence_ecoli NODE_2_length_652771_cov_13.1584 106180..107064
Sample5 terC 90.62 714 / 714 Tellurium ion resistance protein CP000468 virulence_ecoli NODE_2_length_652771_cov_13.1584 516935..517648
Sample5 terC 94.26 959 / 966 Tellurium ion resistance protein MG591698 virulence_ecoli NODE_2_length_652771_cov_13.1584 171617..172575
Sample5 tir 98.39 1617 / 1617 Translocated intimin receptor protein AJ303141 virulence_ecoli NODE_9_length_234966_cov_12.9153 41663..43279


Sample7

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample7 ace 96.99 2025 / 2025 collagen adhesin precursor AE016830.1 virulence_ent 4 length=199313 depth=0.88x 46753..48777
Sample7 agg 95.52 3836 / 3918 aggregation substance CP002493.1 virulence_ent 14 length=50586 depth=7.27x circular=true 11075..14908
Sample7 cad 100.00 930 / 930 CP003726.1 virulence_ent 6 length=190520 depth=1.28x 28624..29553
Sample7 camE 100.00 501 / 501 sex pheromone cAM373 precursor AF435440.1 virulence_ent 1 length=711170 depth=0.76x 614567..615067
Sample7 camE 100.00 501 / 501 sex pheromone cAM373 precursor AF435441.1 virulence_ent 1 length=711170 depth=0.76x 614567..615067
Sample7 cCF10 100.00 828 / 828 CP003726.1 virulence_ent 11 length=120076 depth=1.34x 51550..52377
Sample7 cOB1 100.00 819 / 819 CP002491.1 virulence_ent 9 length=150146 depth=1.05x 1964..2782
Sample7 ebpA 100.00 3312 / 3312 CP003726.1 virulence_ent 4 length=199313 depth=0.88x 33894..37205
Sample7 ebpC 100.00 1884 / 1884 CP002491.1 virulence_ent 4 length=199313 depth=0.88x 38636..40519
Sample7 efaAfs 100.00 927 / 927 FP929058.1 virulence_ent 1 length=711170 depth=0.76x 41749..42675
Sample7 ElrA 100.00 2172 / 2172 CP003726.1 virulence_ent 10 length=142706 depth=1.09x 137447..139618
Sample7 gelE 99.87 1531 / 1530 CP002491.1 virulence_ent 1 length=711170 depth=0.76x 201368..202898
Sample7 hylA 100.00 3266 / 3266 CP003726.1 virulence_ent 12 length=82155 depth=1.17x 22773..26038
Sample7 hylB 99.57 3015 / 3015 CP002621.1 virulence_ent 3 length=232179 depth=1.11x 14836..17850
Sample7 SrtA 100.00 735 / 735 CP003726.1 virulence_ent 12 length=82155 depth=1.17x 49786..50520
Sample7 tpx 100.00 510 / 510 CP003726.1 virulence_ent 13 length=55954 depth=1.10x 38845..39354


Sample8

Sample Gene Identity Coverage Product Accession Database Contig Position.in.contig
Sample8 ace 97.59 1743 / 1743 collagen adhesin precursor AF260879.1 virulence_ent 2 length=425404 depth=0.79x 28094..29836
Sample8 agg 95.15 3177 / 3918 aggregation substance CP002493.1 virulence_ent 22 length=14830 depth=1.11x 10917..14090
Sample8 cad 99.89 930 / 930 CP003726.1 virulence_ent 5 length=166051 depth=1.36x 137031..137960
Sample8 camE 99.80 501 / 501 sex pheromone cAM373 precursor AF435437.1 virulence_ent 2 length=425404 depth=0.79x 269211..269711
Sample8 camE 99.80 501 / 501 sex pheromone cAM373 precursor AF435438.1 virulence_ent 2 length=425404 depth=0.79x 269211..269711
Sample8 cCF10 100.00 828 / 828 FP929058.1 virulence_ent 3 length=261651 depth=1.43x 215799..216626
Sample8 cOB1 100.00 819 / 819 295112306 virulence_ent 1 length=805442 depth=0.90x 657730..658548
Sample8 ebpA 99.97 3312 / 3312 295112306 virulence_ent 16 length=30495 depth=0.88x 13027..16338
Sample8 ebpC 100.00 1884 / 1884 295112306 virulence_ent 16 length=30495 depth=0.88x 9713..11596
Sample8 efaAfs 99.89 927 / 927 CP002491.1 virulence_ent 1 length=805442 depth=0.90x 386430..387356
Sample8 ElrA 99.72 2172 / 2172 CP003726.1 virulence_ent 8 length=139043 depth=1.14x 1540..3711
Sample8 hylA 99.58 3116 / 3264 CP002491.1 virulence_ent 10 length=81793 depth=1.28x 2..3117
Sample8 SrtA 100.00 735 / 735 295112306 virulence_ent 10 length=81793 depth=1.28x 22880..23614
Sample8 tpx 99.80 507 / 510 295112306 virulence_ent 13 length=38545 depth=1.24x 15725..16231


Virulence Factors Heatmaps

VFDB

VirulenceFinder

Plasmids

Plasmidfinder

Sample1

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample1 IncHI1B_1_pNDM-MAR IncHI1B_1_pNDM-MAR_JN420336 100 99.47 NODE_33_length_64036_cov_21.829062 7709 8278 \(-\) 1-570/570 0/0 JN420336 NA
Sample1 IncFIB(Mar)_1_pNDM-Mar IncFIB(Mar)_1_pNDM-Mar_JN420336 100 99.54 NODE_37_length_41339_cov_22.613615 1879 2317 \(+\) 1-439/439 0/0 JN420336 NA
Sample1 IncFIB(pQil)_1_pQil IncFIB(pQil)_1_pQil_JN233705 100 100.00 NODE_52_length_13850_cov_19.421186 9468 10207 \(+\) 1-740/740 0/0 JN233705 NA
Sample1 ColRNAI_1 ColRNAI_1__DQ298019 100 100.00 NODE_57_length_9371_cov_180.047773 9009 9138 \(-\) 1-130/130 0/0 DQ298019 NA
Sample1 IncFIB(K)_1_Kpn3 IncFIB(K)_1_Kpn3_JN233704 100 100.00 NODE_58_length_8138_cov_20.634164 3477 4036 \(-\) 1-560/560 0/0 JN233704 NA


Sample2

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample2 IncHI1B_1_pNDM-MAR IncHI1B_1_pNDM-MAR_JN420336 100.00 99.83 NODE_33_length_50445_cov_22.742555 46660 47229 \(-\) 1-570/570 0/0 JN420336 NA
Sample2 IncFIB(Mar)_1_pNDM-Mar IncFIB(Mar)_1_pNDM-Mar_JN420336 100.00 99.54 NODE_34_length_47768_cov_20.922962 44144 44582 \(-\) 1-439/439 0/0 JN420336 NA
Sample2 IncR_1 IncR_1__DQ449578 100.00 100.00 NODE_55_length_11051_cov_46.535174 5301 5551 \(-\) 1-251/251 0/0 DQ449578 NA
Sample2 ColRNAI_1 ColRNAI_1__DQ298019 100.00 100.00 NODE_57_length_9371_cov_158.965677 8431 8560 \(-\) 1-130/130 0/0 DQ298019 NA
Sample2 Col440I_1 Col440I_1__CP023920.1 97.37 90.99 NODE_68_length_5436_cov_320.203023 3269 3379 \(-\) 1-111/114 0/0 CP023920.1 NA
Sample2 Col440II_1 Col440II_1__CP023921.1 100.00 99.29 NODE_68_length_5436_cov_320.203023 3997 4278 \(-\) 1-282/282 0/0 CP023921.1 NA


Sample3

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample3 rep16_3_rep(pSaa6159) rep16_3_rep(pSaa6159)_CP002115 100 99.87 NODE_104_length_1186_cov_612.692308 148 891 \(-\) 1-744/744 0/0 CP002115 NA
Sample3 rep5a_1_repSAP001(pN315) rep5a_1_repSAP001(pN315)_AP003139 100 99.88 NODE_82_length_4330_cov_505.471111 117 977 \(+\) 1-861/861 0/0 AP003139 NA
Sample3 rep5a_1_repSAP001(pN315) rep5a_1_repSAP001(pN315)_AP003139 100 99.88 NODE_82_length_4330_cov_505.471111 3354 4214 \(-\) 1-861/861 0/0 AP003139 NA


Sample5

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample5 IncI_Gamma_1 IncI_Gamma_1_AP011954 97.16 97.81 NODE_17_length_99884_cov_10.8751 16556 16692 \(-\) 5-141/141 0/0 AP011954 NA


Sample7

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample7 rep8b_1_repA(pEJ97p1) rep8b_1_repA(pEJ97p1)_AJ49170 100 97.76 14 1 984 \(+\) 1-984/984 0/0 AJ49170 NA


Sample8

Sample Plasmid Product Coverage Identity Sequence Start End Strand N.Coverage Gaps Accession Resistance
Sample8 rep6_1_repA(pS86) rep6_1_repA(pS86)_AJ223161 100 100 26 1 723 \(+\) 1-723/723 0/0 AJ223161 NA


Escherichia

ECtyper

Sample O.type H.type Alleles
Sample5 O65 wzx: 1.00 wzy: 1.00

Kleborate

Sample enterobacterales__species__species escherichia__mlst_achtman__ST escherichia__mlst_achtman__clonal_complex escherichia__mlst_achtman__adk escherichia__mlst_achtman__fumC escherichia__mlst_achtman__gyrB escherichia__mlst_achtman__icd escherichia__mlst_achtman__mdh escherichia__mlst_achtman__purA escherichia__mlst_achtman__recA escherichia__mlst_pasteur__ST escherichia__mlst_pasteur__dinB escherichia__mlst_pasteur__icdA escherichia__mlst_pasteur__pabB escherichia__mlst_pasteur__polB escherichia__mlst_pasteur__putP escherichia__mlst_pasteur__trpA escherichia__mlst_pasteur__trpB escherichia__mlst_pasteur__uidA
Sample5 Escherichia albertii ST6057 NA 163 787 134 189 280 149 75 NA 138* 228* 177* 119* 141* 257* 124* \(-\)

EcOH

Sample Gene Coverage_Percentage Identity_Percentage Accession Product Resistance Sequence Start End Strand Coverage Coverage_map Gaps
Sample5 wzx-O65 100 97.84 AB812026.1 O antigen flippase O65 NA NODE_19_length_94323_cov_11.8685 23063 24313 \(+\) 1-1251/1251 =============== 0/0
Sample5 wzy-O65 100 98.03 AB812026.1 O antigen polyermase O65 NA NODE_19_length_94323_cov_11.8685 28233 29504 \(+\) 1-1272/1272 =============== 0/0

Ecoli_VF

Sample Gene Coverage_Percentage Identity_Percentage Accession Product Resistance Sequence Start End Strand Coverage Coverage_map Gaps
Sample5 fliQ 99.63 92.56 gi:15802384 flagellar biosynthesis protein FliQ NA NODE_11_length_157119_cov_12.3018 28408 28676 \(-\) 1-269/270 =============== 0/0
Sample5 fliN 100.00 90.58 gi:15802381 flagellar motor switch protein FliN NA NODE_11_length_157119_cov_12.3018 29790 30203 \(-\) 1-414/414 =============== 0/0
Sample5 fliJ 100.00 95.50 gi:15802377 flagellar biosynthesis chaperone NA NODE_11_length_157119_cov_12.3018 32890 33333 \(-\) 1-444/444 =============== 0/0
Sample5 fliI 100.00 90.97 gi:161367587 flagellum-specific ATP synthase NA NODE_11_length_157119_cov_12.3018 33352 34725 \(-\) 1-1374/1374 =============== 0/0
Sample5 fliG 100.00 91.17 gi:15802374 flagellar motor switch protein G NA NODE_11_length_157119_cov_12.3018 35404 36399 \(-\) 1-996/996 =============== 0/0
Sample5 fliS 100.00 90.27 gi:15802360 flagellar protein FliS NA NODE_11_length_157119_cov_12.3018 44781 45191 \(-\) 1-411/411 =============== 0/0
Sample5 fliD 99.57 90.83 gi:15802359 flagellar capping protein NA NODE_11_length_157119_cov_12.3018 45216 46616 \(-\) 1-1398/1398 ========/====== 2/15
Sample5 fliA 100.00 94.03 gi:15802357 flagellar biosynthesis sigma factor NA NODE_11_length_157119_cov_12.3018 48542 49261 \(+\) 1-720/720 =============== 0/0
Sample5 fliY 100.00 90.51 gi:15802355 cystine transporter subunit NA NODE_11_length_157119_cov_12.3018 49946 50746 \(+\) 1-801/801 =============== 0/0
Sample5 flhA 100.00 90.52 gi:15802291 flagellar biosynthesis protein FlhA NA NODE_11_length_157119_cov_12.3018 118794 120872 \(+\) 1-2079/2079 =============== 0/0
Sample5 ibeC 100.00 90.05 gi:91213503 hypothetical protein NA NODE_13_length_125154_cov_13.4191 18855 20633 \(+\) 1-1779/1779 =============== 0/0
Sample5 csgG 100.00 90.29 VFG045788 curli production assembly/transport component CsgG NA NODE_15_length_121660_cov_15.1866 9254 10087 \(-\) 1-834/834 =============== 0/0
Sample5 csgE 100.00 92.56 gi:15801156 curli assembly protein CsgE NA NODE_15_length_121660_cov_15.1866 10554 10943 \(-\) 1-390/390 =============== 0/0
Sample5 csgD 100.00 91.86 gi:15801157 DNA-binding transcriptional regulator CsgD NA NODE_15_length_121660_cov_15.1866 10948 11598 \(-\) 1-651/651 =============== 0/0
Sample5 csgB 100.00 95.65 VFG045792 minor curlin subunit CsgB NA NODE_15_length_121660_cov_15.1866 12327 12809 \(+\) 1-483/483 =============== 0/0
Sample5 csgA 99.35 94.34 VFG045793 curlin major subunit CsgA NA NODE_15_length_121660_cov_15.1866 12850 13305 \(+\) 1-459/459 ========/====== 1/3
Sample5 flgB 100.00 92.33 gi:15801190 flagellar basal body rod protein FlgB NA NODE_15_length_121660_cov_15.1866 37503 37919 \(+\) 1-417/417 =============== 0/0
Sample5 flgG 100.00 91.70 gi:15801195 flagellar basal body rod protein FlgG NA NODE_15_length_121660_cov_15.1866 41193 41975 \(+\) 1-783/783 =============== 0/0
Sample5 flgJ 100.00 90.23 gi:15801198 flagellar rod assembly protein/muramidase FlgJ NA NODE_15_length_121660_cov_15.1866 43837 44778 \(+\) 1-942/942 =============== 0/0
Sample5 ycfz 100.00 93.66 SPG000092 putative factor NA NODE_15_length_121660_cov_15.1866 83617 84405 \(-\) 1-789/789 =============== 0/0
Sample5 Z1307 100.00 94.40 gi:15800816 outer membrane protein A NA NODE_1_length_833323_cov_12.8744 75770 76822 \(+\) 1-1041/1041 ========/====== 1/12
Sample5 entA 100.00 92.24 gi:26246575 23-dihydro-23-dihydroxybenzoate dehydrogenase NA NODE_1_length_833323_cov_12.8744 505781 506527 \(-\) 1-747/747 =============== 0/0
Sample5 entB 100.00 92.89 gi:26246574 isochorismatase NA NODE_1_length_833323_cov_12.8744 506527 507384 \(-\) 1-858/858 =============== 0/0
Sample5 entE 100.00 91.19 gi:26246573 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex NA NODE_1_length_833323_cov_12.8744 507398 509008 \(-\) 1-1611/1611 =============== 0/0
Sample5 entC 100.00 90.15 gi:26246572 isochorismate synthase 1 NA NODE_1_length_833323_cov_12.8744 509018 510205 \(-\) 1-1188/1188 =============== 0/0
Sample5 fepB 100.00 91.64 gi:26246571 ferrienterobactin ABC transporter periplasmic binding protein NA NODE_1_length_833323_cov_12.8744 510382 511338 \(+\) 1-957/957 =============== 0/0
Sample5 entS 100.00 94.88 gi:26246570 enterobactin exporter iron-regulated NA NODE_1_length_833323_cov_12.8744 511342 512592 \(-\) 1-1251/1251 =============== 0/0
Sample5 fepD 100.00 92.23 gi:26246569 ferrienterobactin ABC transporter permease NA NODE_1_length_833323_cov_12.8744 512691 513707 \(+\) 1-1017/1017 =============== 0/0
Sample5 fepG 100.00 92.35 gi:26246568 iron-enterobactin ABC transporter permease NA NODE_1_length_833323_cov_12.8744 513704 514696 \(+\) 1-993/993 =============== 0/0
Sample5 fepC 100.00 93.63 gi:26246567 ferrienterobactin ABC transporter ATPase NA NODE_1_length_833323_cov_12.8744 514693 515508 \(+\) 1-816/816 =============== 0/0
Sample5 fes 100.00 90.61 gi:26246563 enterobactin/ferric enterobactin esterase NA NODE_1_length_833323_cov_12.8744 520960 522162 \(-\) 1-1203/1203 =============== 0/0
Sample5 fepA 100.00 90.76 gi:26246561 ferrienterobactin outer membrane transporter NA NODE_1_length_833323_cov_12.8744 522403 524652 \(+\) 1-2241/2241 ========/====== 1/9
Sample5 ibeB 99.93 98.12 gi:26246550 copper/silver efflux system outer membrane protein CusC NA NODE_1_length_833323_cov_12.8744 536459 537840 \(-\) 1-1382/1383 =============== 0/0
Sample5 ehaB 100.00 95.50 gi:260842574 flagellin structural protein NA NODE_1_length_833323_cov_12.8744 700496 703474 \(-\) 1-2979/2979 =============== 0/0
Sample5 clpV 99.93 93.04 gi:218693685 ATP-dependent Clp proteinase Aec27 ATP-binding chain with chaperone activity NA NODE_23_length_31603_cov_13.4482 17887 20758 \(-\) 3-2874/2874 =============== 0/0
Sample5 aec26 100.00 90.29 gi:260853429 hypothetical protein NA NODE_23_length_31603_cov_13.4482 20655 21416 \(-\) 1-762/762 =============== 0/0
Sample5 aec25 100.00 90.69 gi:15799905 hypothetical protein NA NODE_23_length_31603_cov_13.4482 21421 22752 \(-\) 1-1332/1332 =============== 0/0
Sample5 aec24 100.00 90.86 gi:15799906 hypothetical protein NA NODE_23_length_31603_cov_13.4482 22755 23279 \(-\) 1-525/525 =============== 0/0
Sample5 aec22 100.00 91.37 gi:218693690 hypothetical protein NA NODE_23_length_31603_cov_13.4482 24581 25669 \(-\) 1-1089/1089 =============== 0/0
Sample5 aec18 99.39 90.65 gi:410484140 hypothetical protein NA NODE_23_length_31603_cov_13.4482 27901 29367 \(-\) 1-1476/1476 ========/====== 1/9
Sample5 hcp 100.00 90.37 gi:15799915 hypothetical protein NA NODE_23_length_31603_cov_13.4482 30808 31326 \(+\) 1-519/519 =============== 0/0
Sample5 ECS88_3547 100.00 98.53 gi:218560235 lipoprotein NlpI NA NODE_2_length_652771_cov_13.1584 106180 107064 \(+\) 1-885/885 =============== 0/0
Sample5 yghg 100.00 93.92 SPG000136 Pilotin Secretion system Type II Secretion System NA NODE_2_length_652771_cov_13.1584 327823 328233 \(+\) 1-411/411 =============== 0/0
Sample5 gspC 100.00 91.04 gi:157156659 putative type II secretion protein GspC NA NODE_2_length_652771_cov_13.1584 328251 329210 \(+\) 1-960/960 =============== 0/0
Sample5 gspD 100.00 92.53 gi:157157281 general secretion pathway protein D NA NODE_2_length_652771_cov_13.1584 329240 331300 \(+\) 1-2061/2061 =============== 0/0
Sample5 gspE 100.00 93.71 gi:157159001 general secretory pathway protein E NA NODE_2_length_652771_cov_13.1584 331300 332793 \(+\) 1-1494/1494 =============== 0/0
Sample5 gspF 100.00 92.40 gi:157154920 general secretion pathway protein F NA NODE_2_length_652771_cov_13.1584 332793 334016 \(+\) 1-1224/1224 =============== 0/0
Sample5 gspG 100.00 93.20 gi:157157959 general secretion pathway protein G NA NODE_2_length_652771_cov_13.1584 334033 334488 \(+\) 1-456/456 =============== 0/0
Sample5 gspI 100.00 90.32 gi:157156956 general secretion pathway protein I NA NODE_2_length_652771_cov_13.1584 335052 335423 \(+\) 1-372/372 =============== 0/0
Sample5 gspJ 99.33 90.94 gi:157157609 general secretion pathway protein J NA NODE_2_length_652771_cov_13.1584 335420 336015 \(+\) 1-596/600 =============== 0/0
Sample5 gspK 100.00 91.00 gi:157155920 general secretion pathway protein K NA NODE_2_length_652771_cov_13.1584 336022 336999 \(+\) 1-978/978 =============== 0/0
Sample5 yggr 100.00 90.62 SPG000074 Retraction ATPase Adherence Hemorrhagic coli pilus NA NODE_2_length_652771_cov_13.1584 367230 368210 \(+\) 1-981/981 =============== 0/0
Sample5 cdtA 100.00 99.36 gi:436945 CdtA NA NODE_4_length_290048_cov_13.1184 54090 54866 \(+\) 1-777/777 =============== 0/0
Sample5 cdtB 100.00 99.01 gi:436946 CdtB NA NODE_4_length_290048_cov_13.1184 54863 55672 \(+\) 1-810/810 =============== 0/0
Sample5 cdtC 100.00 98.17 gi:436947 CdtC NA NODE_4_length_290048_cov_13.1184 55687 56232 \(+\) 1-546/546 =============== 0/0
Sample5 iss2 98.06 90.76 SPG000143 Escherichia coli Iss (iss) gene complete cds. NA NODE_5_length_284821_cov_12.9843 246793 247095 \(+\) 6-308/309 =============== 0/0
Sample5 espM2 100.00 97.12 gi:15803143 Type III secretion system effector EspM2 Rho guanine exchange factor NA NODE_5_length_284821_cov_12.9843 280887 281477 \(-\) 1-591/591 =============== 0/0
Sample5 nleG8-2 100.00 93.55 gi:260844213 T3SS effector NleG NA NODE_5_length_284821_cov_12.9843 281661 282311 \(+\) 1-651/651 =============== 0/0
Sample5 espW 100.00 97.07 gi:260844214 T3SS effector EspW NA NODE_5_length_284821_cov_12.9843 282388 283446 \(+\) 1-1059/1059 =============== 0/0
Sample5 cadA 100.00 96.60 SPG000027 gb|AY319765.1|:1081-3256 Escherichia coli cadBA operon partial sequence NA NODE_7_length_258688_cov_13.1509 119177 121352 \(-\) 1-2176/2176 =============== 0/0
Sample5 chuA 100.00 90.42 gi:110643744 outer membrane hemin receptor NA NODE_8_length_237146_cov_13.3532 218913 220895 \(-\) 1-1983/1983 =============== 0/0
Sample5 chuT 98.89 90.21 gi:218702267 putative periplasmic binding protein NA NODE_8_length_237146_cov_13.3532 221512 222502 \(+\) 12-993/993 ========/====== 1/9
Sample5 chuW 100.00 92.45 gi:215488780 coproporphyrinogen III oxidase NA NODE_8_length_237146_cov_13.3532 222522 223859 \(+\) 1-1338/1338 =============== 0/0
Sample5 chuU 100.00 91.44 gi:387609230 putative iron compound ABC transporter permease NA NODE_8_length_237146_cov_13.3532 225040 226032 \(+\) 1-993/993 =============== 0/0
Sample5 ECO103_3640 100.00 98.90 gi:260845719 T3SS component NA NODE_9_length_234966_cov_12.9153 19772 20590 \(-\) 1-819/819 =============== 0/0
Sample5 espG 100.00 99.50 gi:260858241 T3SS effector EspG NA NODE_9_length_234966_cov_12.9153 20737 21933 \(-\) 1-1197/1197 =============== 0/0
Sample5 ler 100.00 100.00 gi:260845717 transcription regulator Ler NA NODE_9_length_234966_cov_12.9153 23070 23459 \(+\) 1-390/390 =============== 0/0
Sample5 ECO103_3637 100.00 100.00 gi:260845716 T3SS component NA NODE_9_length_234966_cov_12.9153 23474 23692 \(+\) 1-219/219 =============== 0/0
Sample5 ECO103_3636 100.00 100.00 gi:260845715 T3SS component NA NODE_9_length_234966_cov_12.9153 23705 24019 \(+\) 1-315/315 =============== 0/0
Sample5 ECO103_3635 100.00 99.33 gi:260845714 T3SS component NA NODE_9_length_234966_cov_12.9153 24016 24615 \(+\) 1-600/600 =============== 0/0
Sample5 ECO103_3634 100.00 99.57 gi:260845713 T3SS component NA NODE_9_length_234966_cov_12.9153 24560 25255 \(+\) 1-696/696 =============== 0/0
Sample5 escR 100.00 99.85 gi:260845712 T3SS structure protein EscR NA NODE_9_length_234966_cov_12.9153 25260 25913 \(+\) 1-654/654 =============== 0/0
Sample5 escS 100.00 100.00 gi:260845711 T3SS structure protein EscS NA NODE_9_length_234966_cov_12.9153 25913 26182 \(+\) 1-270/270 =============== 0/0
Sample5 escT 100.00 99.61 gi:260845710 T3SS structure protein EscT NA NODE_9_length_234966_cov_12.9153 26182 26958 \(+\) 1-777/777 =============== 0/0
Sample5 escU 100.00 99.61 gi:260845709 T3SS structure protein EscU NA NODE_9_length_234966_cov_12.9153 26951 27988 \(+\) 1-1038/1038 =============== 0/0
Sample5 ECO103_3629 100.00 99.78 gi:260845708 hypothetical protein NA NODE_9_length_234966_cov_12.9153 27985 28443 \(-\) 1-459/459 =============== 0/0
Sample5 glrR 100.00 99.72 gi:260858252 negative regulator GrlR NA NODE_9_length_234966_cov_12.9153 28640 28996 \(+\) 1-357/357 =============== 0/0
Sample5 glrA 100.00 99.76 gi:260845706 positive regulator GrlA NA NODE_9_length_234966_cov_12.9153 29072 29485 \(+\) 1-414/414 =============== 0/0
Sample5 cesD 100.00 99.78 gi:260845705 chaperone CesD NA NODE_9_length_234966_cov_12.9153 29871 30326 \(-\) 1-456/456 =============== 0/0
Sample5 escC 100.00 99.48 gi:260845704 T3SS structure protein EscC NA NODE_9_length_234966_cov_12.9153 30340 31878 \(-\) 1-1539/1539 =============== 0/0
Sample5 sepD 100.00 99.56 gi:260845703 secretion switching protein SepD NA NODE_9_length_234966_cov_12.9153 31878 32333 \(-\) 1-456/456 =============== 0/0
Sample5 escJ 100.00 97.73 gi:260845702 T3SS structure protein EscJ NA NODE_9_length_234966_cov_12.9153 32339 32911 \(-\) 1-573/573 =============== 0/0
Sample5 rorf8 100.00 98.60 gi:260858258 T3SS component NA NODE_9_length_234966_cov_12.9153 32914 33342 \(-\) 1-429/429 =============== 0/0
Sample5 sepZ 100.00 99.01 gi:260858259 T3SS effector EspZ NA NODE_9_length_234966_cov_12.9153 33375 33677 \(-\) 1-303/303 =============== 0/0
Sample5 mpc 100.00 99.15 gi:260858260 regulator Mpc NA NODE_9_length_234966_cov_12.9153 33861 34214 \(+\) 1-354/354 =============== 0/0
Sample5 escV 100.00 98.72 gi:260858261 T3SS structure protein EscV NA NODE_9_length_234966_cov_12.9153 34211 36238 \(+\) 1-2028/2028 =============== 0/0
Sample5 escN 100.00 99.70 gi:260845697 translocator EscN NA NODE_9_length_234966_cov_12.9153 36222 37562 \(+\) 1-1341/1341 =============== 0/0
Sample5 ECO103_3617 100.00 99.47 gi:260845696 T3SS component NA NODE_9_length_234966_cov_12.9153 37565 37942 \(+\) 1-378/378 =============== 0/0
Sample5 ECO103_3616 100.00 100.00 gi:260845695 T3SS component NA NODE_9_length_234966_cov_12.9153 37935 38351 \(+\) 1-417/417 =============== 0/0
Sample5 sepQ 100.00 99.67 gi:260858265 T3SS structure protein SepQ NA NODE_9_length_234966_cov_12.9153 38314 39231 \(+\) 1-918/918 =============== 0/0
Sample5 espH 100.00 100.00 gi:260858266 T3SS effector EspH NA NODE_9_length_234966_cov_12.9153 39262 39777 \(+\) 1-516/516 =============== 0/0
Sample5 cesF 100.00 98.89 gi:260845692 chaperone CesF NA NODE_9_length_234966_cov_12.9153 39996 40355 \(-\) 1-360/360 =============== 0/0
Sample5 map 100.00 99.51 gi:260845691 T3SS effector Map NA NODE_9_length_234966_cov_12.9153 40605 41216 \(+\) 1-612/612 =============== 0/0
Sample5 tir 100.00 98.39 gi:260845690 translocated intimin receptor Tir NA NODE_9_length_234966_cov_12.9153 41663 43279 \(+\) 1-1617/1617 =============== 0/0
Sample5 cesT 100.00 100.00 gi:260845689 chaperone CesT NA NODE_9_length_234966_cov_12.9153 43412 43882 \(+\) 1-471/471 =============== 0/0
Sample5 eae 100.00 92.42 gi:260869677 theta intimin NA NODE_9_length_234966_cov_12.9153 43943 46750 \(+\) 1-2808/2808 =============== 0/0
Sample5 escD 100.00 99.18 gi:260858272 T3SS structure protein EscD NA NODE_9_length_234966_cov_12.9153 47046 48266 \(-\) 1-1221/1221 =============== 0/0
Sample5 sepL 100.00 99.81 gi:260858273 secretion switching protein SepL NA NODE_9_length_234966_cov_12.9153 48409 49464 \(+\) 1-1056/1056 =============== 0/0
Sample5 espA 100.00 97.58 gi:260845685 translocon EspA NA NODE_9_length_234966_cov_12.9153 49522 50100 \(+\) 1-579/579 =============== 0/0
Sample5 espD 100.00 99.56 gi:260858275 translocator EspD NA NODE_9_length_234966_cov_12.9153 50113 51255 \(+\) 1-1143/1143 =============== 0/0
Sample5 espB 100.00 99.79 gi:260845683 translocon EspB NA NODE_9_length_234966_cov_12.9153 51276 52220 \(+\) 1-945/945 =============== 0/0
Sample5 cesD2 100.00 100.00 gi:260845682 chaperone CesD2 NA NODE_9_length_234966_cov_12.9153 52227 52634 \(+\) 1-408/408 =============== 0/0
Sample5 escF 100.00 100.00 gi:260845681 T3SS structure protein EscF NA NODE_9_length_234966_cov_12.9153 52671 52892 \(+\) 1-222/222 =============== 0/0
Sample5 ECO103_3601 100.00 99.64 gi:260845680 T3SS component NA NODE_9_length_234966_cov_12.9153 52898 53176 \(+\) 1-279/279 =============== 0/0
Sample5 nleG-1 100.00 99.84 gi:260845677 T3SS effector NleG NA NODE_9_length_234966_cov_12.9153 55107 55745 \(+\) 1-639/639 =============== 0/0
Sample5 nleB1 100.00 90.00 gi:387508332 non-LEE encoded effector protein NleB NA NODE_9_length_234966_cov_12.9153 221536 222525 \(+\) 1-990/990 =============== 0/0
Sample5 nleE 100.00 90.96 gi:15803521 Type III secretion system effector NleE NA NODE_9_length_234966_cov_12.9153 222560 223234 \(+\) 1-675/675 =============== 0/0

Klebsiella

Kleborate

Sample enterobacterales__species__species general__contig_stats__QC_warnings klebsiella_pneumo_complex__mlst__ST klebsiella_pneumo_complex__mlst__gapA klebsiella_pneumo_complex__mlst__infB klebsiella_pneumo_complex__mlst__mdh klebsiella_pneumo_complex__mlst__pgi klebsiella_pneumo_complex__mlst__phoE klebsiella_pneumo_complex__mlst__rpoB klebsiella_pneumo_complex__mlst__tonB klebsiella__ybst__YbST klebsiella__ybst__Yersiniabactin klebsiella__ybst__ybtS klebsiella__ybst__ybtX klebsiella__ybst__ybtQ klebsiella__ybst__ybtP klebsiella__ybst__ybtA klebsiella__ybst__irp2 klebsiella__ybst__irp1 klebsiella__ybst__ybtU klebsiella__ybst__ybtT klebsiella__ybst__ybtE klebsiella__ybst__fyuA klebsiella__ybst__spurious_ybt_hits klebsiella__cbst__CbST klebsiella__cbst__Colibactin klebsiella__cbst__clbA klebsiella__cbst__clbB klebsiella__cbst__clbC klebsiella__cbst__clbD klebsiella__cbst__clbE klebsiella__cbst__clbF klebsiella__cbst__clbG klebsiella__cbst__clbH klebsiella__cbst__clbI klebsiella__cbst__clbL klebsiella__cbst__clbM klebsiella__cbst__clbN klebsiella__cbst__clbO klebsiella__cbst__clbP klebsiella__cbst__clbQ klebsiella__cbst__spurious_clb_hits klebsiella__abst__AbST klebsiella__abst__Aerobactin klebsiella__abst__iucA klebsiella__abst__iucB klebsiella__abst__iucC klebsiella__abst__iucD klebsiella__abst__iutA klebsiella__abst__spurious_abst_hits klebsiella__smst__SmST klebsiella__smst__Salmochelin klebsiella__smst__iroB klebsiella__smst__iroC klebsiella__smst__iroD klebsiella__smst__iroN klebsiella__smst__spurious_smst_hits klebsiella__rmst__RmST klebsiella__rmst__RmpADC klebsiella__rmst__rmpA klebsiella__rmst__rmpD klebsiella__rmst__rmpC klebsiella__rmst__spurious_rmst_hits klebsiella_pneumo_complex__virulence_score__virulence_score klebsiella_pneumo_complex__virulence_score__spurious_virulence_hits klebsiella__rmpa2__rmpA2 klebsiella_pneumo_complex__amr__AGly_acquired klebsiella_pneumo_complex__amr__Col_acquired klebsiella_pneumo_complex__amr__Fcyn_acquired klebsiella_pneumo_complex__amr__Flq_acquired klebsiella_pneumo_complex__amr__Gly_acquired klebsiella_pneumo_complex__amr__MLS_acquired klebsiella_pneumo_complex__amr__Phe_acquired klebsiella_pneumo_complex__amr__Rif_acquired klebsiella_pneumo_complex__amr__Sul_acquired klebsiella_pneumo_complex__amr__Tet_acquired klebsiella_pneumo_complex__amr__Tgc_acquired klebsiella_pneumo_complex__amr__Tmt_acquired klebsiella_pneumo_complex__amr__Bla_acquired klebsiella_pneumo_complex__amr__Bla_inhR_acquired klebsiella_pneumo_complex__amr__Bla_ESBL_acquired klebsiella_pneumo_complex__amr__Bla_ESBL_inhR_acquired klebsiella_pneumo_complex__amr__Bla_Carb_acquired klebsiella_pneumo_complex__amr__Bla_chr klebsiella_pneumo_complex__amr__SHV_mutations klebsiella_pneumo_complex__amr__Omp_mutations klebsiella_pneumo_complex__amr__Col_mutations klebsiella_pneumo_complex__amr__Flq_mutations klebsiella_pneumo_complex__amr__truncated_resistance_hits klebsiella_pneumo_complex__amr__spurious_resistance_hits klebsiella_pneumo_complex__resistance_score__resistance_score klebsiella_pneumo_complex__resistance_class_count__num_resistance_classes klebsiella_pneumo_complex__resistance_gene_count__num_resistance_genes klebsiella_pneumo_complex__wzi__wzi klebsiella_pneumo_complex__kaptive__K_locus klebsiella_pneumo_complex__kaptive__K_type klebsiella_pneumo_complex__kaptive__K_locus_confidence klebsiella_pneumo_complex__kaptive__K_locus_problems klebsiella_pneumo_complex__kaptive__K_locus_identity klebsiella_pneumo_complex__kaptive__K_Missing_expected_genes klebsiella_pneumo_complex__kaptive__O_locus klebsiella_pneumo_complex__kaptive__O_type klebsiella_pneumo_complex__kaptive__O_locus_confidence klebsiella_pneumo_complex__kaptive__O_locus_problems klebsiella_pneumo_complex__kaptive__O_locus_identity klebsiella_pneumo_complex__kaptive__O_Missing_expected_genes
Sample1 Klebsiella pneumoniae \(-\) ST35 2 1 2 1 10 1 19 10 ybt 5; ICEKp6 10 8 10 7 18 4 288 7 8 5 37 \(-\) 0 \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) 63 iuc 1 1 15 1 1 1 \(-\) 0 \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) 0 \(-\) 40*-60% \(-\) \(-\) \(-\) 4 \(-\) rmpA2_6-60% aph(3’)-VI;armA \(-\) \(-\) qnrS1 \(-\) Mrx;mphA*;mphE.v2;msrE \(-\) \(-\) sul1;sul2 \(-\) \(-\) dfrA5 TEM-1D.v1^ \(-\) \(-\) \(-\) KPC-3;NDM-1 SHV-1^ \(-\) \(-\) \(-\) \(-\) OXA-9.v1*-42% \(-\) 2 7 13 wzi37 KL22 K22 Typeable \(-\) 99.79% \(-\) O1/O2v1 O1ab Typeable \(-\) 98.85% \(-\)
Sample2 Klebsiella pneumoniae \(-\) ST101 2 6 1 5 4 1 6 183 ybt 9; ICEKp3 5 11 6 5 1 25 37 9 5 5 11 \(-\) 0 \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) 95 iuc 1 46 1 1 1 1 \(-\) 0 \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) 0 \(-\) 40*-45% \(-\) \(-\) rmpA_1-45%;rmpA_1-0%;rmpA_2-45%;rmpA_2-0%;rmpA_3-45%;rmpA_3-0%;rmpA_4-45%;rmpA_4-0%;rmpA_5-45%;rmpA_5-0%;rmpA_6-45%;rmpA_6-0%;rmpA_7-45%;rmpA_7-0%;rmpA_8-45%;rmpA_8-0%;rmpA_9-45%;rmpA_9-0%;rmpA_10-46%;rmpA_10-0%;rmpA_11-45%;rmpA_12-45%;rmpA_13-45%;rmpA_14-45%;rmpA_14-0%;rmpA_15-45%;rmpA_15-0%;rmpA_16-45%;rmpA_16-0%;rmpA_17-45%;rmpA_17-0%;rmpA_18-45%;rmpA_18-0%;rmpA_19-45%;rmpA_19-0%;rmpA_20-45%;rmpA_21-45%;rmpA_21-0%;rmpA_22-46%;rmpA_22-0%;rmpA_23-45%;rmpA_23-0%;rmpA_24-45%;rmpA_24-0%;rmpA_25-45%;rmpA_25-0%;rmpA_26-45%;rmpA_26-0%;rmpA_27-45%;rmpA_27-0%;rmpA_28-45%;rmpA_28-0%;rmpA_29-46%;rmpA_29-0%;rmpA_30-45%;rmpA_30-0%;rmpA_31-45%;rmpA_31-0%;rmpA_32-45%;rmpA_32-0%;rmpA_33-45%;rmpA_33-0%;rmpA_34-45%;rmpA_34-0%;rmpA_35-46%;rmpA_35-0%;rmpA_36-45%;rmpA_36-0%;rmpA_37-46%;rmpA_38-0%;rmpA_39-0%;rmpA_40-0%;rmpA_41-45%;rmpA_41-0%;rmpA_42-45%;rmpA_42-0%;rmpA_43-45%;rmpA_44-45%;rmpA_44-0%;rmpA_45-45%;rmpA_46-45%;rmpA_46-0%;rmpA_47-0%;rmpA_48-45%;rmpA_49-45%;rmpA_50-45%;rmpA_50-0%;rmpA_51-45%;rmpA_51-0%;rmpA_52-45%;rmpA_52-0%;rmpA_53-0%;rmpA_58-45%;rmpA_58-0%;rmpA_59-45%;rmpA_59-0%;rmpA_60-45%;rmpA_60-0%;rmpA_61-45%;rmpA_61-0%;rmpA_62-45%;rmpA_62-0%;rmpA_63-45%;rmpA_63-0%;rmpA_64-45%;rmpA_64-0%;rmpA_65-45%;rmpA_65-0%;rmpA_66-45%;rmpA_66-0%;rmpA_67-45%;rmpA_67-0%;rmpA_68-45%;rmpA_68-0%;rmpA_69-45%;rmpA_69-0%;rmpA_70-45%;rmpA_70-0%;rmpA_71-45%;rmpA_71-0%;rmpA_72-45%;rmpA_73-45%;rmpA_73-0%;rmpA_74-45%;rmpA_74-0%;rmpA_75-45%;rmpA_76-45%;rmpA_76-0%;rmpA_77-46%;rmpA_77-0%;rmpA_78-45%;rmpA_78-0%;rmpA_79-45%;rmpA_79-0%;rmpA_80-45%;rmpA_80-0%;rmpA_81-45%;rmpA_82-45%;rmpA_82-0%;rmpA_83-45%;rmpA_83-0%;rmpA_84-45%;rmpA_85-45%;rmpA_85-0%;rmpA_86-45%;rmpA_86-0%;rmpA_87-45%;rmpA_87-0%;rmpA_88-45%;rmpA_88-0%;rmpA_89-45%;rmpA_89-0%;rmpA_90-45%;rmpA_91-45%;rmpA_92-45%;rmpA_92-0%;rmpA_93-45%;rmpA_93-0%;rmpA_94-45%;rmpA_95-0%;rmpA_96-45%;rmpA_96-0%;rmpA_97-45%;rmpA_97-0% 4 rmpA_145%;rmpA_10%;rmpA_245%;rmpA_20%;rmpA_345%;rmpA_30%;rmpA_445%;rmpA_40%;rmpA_545%;rmpA_50%;rmpA_645%;rmpA_60%;rmpA_745%;rmpA_70%;rmpA_845%;rmpA_80%;rmpA_945%;rmpA_90%;rmpA_1046%;rmpA_100%;rmpA_1145%;rmpA_1245%;rmpA_1345%;rmpA_1445%;rmpA_140%;rmpA_1545%;rmpA_150%;rmpA_1645%;rmpA_160%;rmpA_1745%;rmpA_170%;rmpA_1845%;rmpA_180%;rmpA_1945%;rmpA_190%;rmpA_2045%;rmpA_2145%;rmpA_210%;rmpA_2246%;rmpA_220%;rmpA_2345%;rmpA_230%;rmpA_2445%;rmpA_240%;rmpA_2545%;rmpA_250%;rmpA_2645%;rmpA_260%;rmpA_2745%;rmpA_270%;rmpA_2845%;rmpA_280%;rmpA_2946%;rmpA_290%;rmpA_3045%;rmpA_300%;rmpA_3145%;rmpA_310%;rmpA_3245%;rmpA_320%;rmpA_3345%;rmpA_330%;rmpA_3445%;rmpA_340%;rmpA_3546%;rmpA_350%;rmpA_3645%;rmpA_360%;rmpA_3746%;rmpA_380%;rmpA_390%;rmpA_400%;rmpA_4145%;rmpA_410%;rmpA_4245%;rmpA_420%;rmpA_4345%;rmpA_4445%;rmpA_440%;rmpA_4545%;rmpA_4645%;rmpA_460%;rmpA_470%;rmpA_4845%;rmpA_4945%;rmpA_5045%;rmpA_500%;rmpA_5145%;rmpA_510%;rmpA_5245%;rmpA_520%;rmpA_530%;rmpA_5845%;rmpA_580%;rmpA_5945%;rmpA_590%;rmpA_6045%;rmpA_600%;rmpA_6145%;rmpA_610%;rmpA_6245%;rmpA_620%;rmpA_6345%;rmpA_630%;rmpA_6445%;rmpA_640%;rmpA_6545%;rmpA_650%;rmpA_6645%;rmpA_660%;rmpA_6745%;rmpA_670%;rmpA_6845%;rmpA_680%;rmpA_6945%;rmpA_690%;rmpA_7045%;rmpA_700%;rmpA_7145%;rmpA_710%;rmpA_7245%;rmpA_7345%;rmpA_730%;rmpA_7445%;rmpA_740%;rmpA_7545%;rmpA_7645%;rmpA_760%;rmpA_7746%;rmpA_770%;rmpA_7845%;rmpA_780%;rmpA_7945%;rmpA_790%;rmpA_8045%;rmpA_800%;rmpA_8145%;rmpA_8245%;rmpA_820%;rmpA_8345%;rmpA_830%;rmpA_8445%;rmpA_8545%;rmpA_850%;rmpA_8645%;rmpA_860%;rmpA_8745%;rmpA_870%;rmpA_8845%;rmpA_880%;rmpA_8945%;rmpA_890%;rmpA_9045%;rmpA_9145%;rmpA_9245%;rmpA_920%;rmpA_9345%;rmpA_930%;rmpA_9445%;rmpA_950%;rmpA_9645%;rmpA_960%;rmpA_9745%;rmpA_970% \(-\) aadA*;ant(2’’)-Ia;armA \(-\) \(-\) \(-\) \(-\) mphE.v2;msrE catA1^ \(-\) sul1 \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) \(-\) KPC-3 SHV-1^ \(-\) OmpK35-17%;OmpK36TD MgrB-0% GyrA-83Y;GyrA-87N;ParC-80I \(-\) \(-\) 3 7 8 wzi137 KL17 K17 Typeable ?2! 100.00% \(-\) O1/O2v1 O1ab Typeable ?2 99.03% \(-\)

Streptococcus Pyogenes

EMMtyper

Sample Number of Clusters Predicted emm-type Possible emm-like alleles EMM clusters
Sample4 1 EMM1.0 NA A-C3
Note:
* Suspect emm-like Allele flagged in the CDC database as possibly emm-like
~ Imperfect score Match score below 100%

Haemophilus influenzae

HICAP

Sample predicted_serotype attributes genes_identified locus_location region_I_genes region_II_genes region_III_genes IS1016_hits
Sample6 type_a missing_genes,truncated_genes acs1,acs2,acs3,acs4 Z37516 Z37516 Haemophilus influenzae serotype a capsulation locus region II DNA.:270-5577 0/4 (missing: bexA,bexC,bexB,bexD) 4/4 0/2 (missing: hcsB,hcsA) 0

Shigella

Shigatyper

Staphylococcus

sccmec

Sample type subtype mecA targets regions coverage hits target_schema target_schema_version region_schema region_schema_version camlhmp_version params target_comment region_comment comment
Sample3 \(-\) \(-\) \(-\) NA NA NA NA sccmec_targets 1.2.0 sccmec_regions 1.2.0 1.1.0 min-targets-coverage=80;min-targets-pident=90;min-regions-coverage=83;min-regions-pident=85 A type could not be determined A type could not be determined A type could not be determined based on the target matches or cassette coverage

spatyper

Sample Sequence Name Repeats Type
Sample3 NODE_17_length_43790_cov_82.750223 08-16-34 t026
Sample3 NODE_1879_length_119_cov_107.203125 34-34-16-34 34-34-16-34

agrvate

Sample agr_group match_score canonical_agrD multiple_agr frameshifts
Sample3 gp1 13 1 s 0

Streptococcus pneumoniae

PBPtyper

Listeria monocytogenes

LisSero

Legionella pneumophila

Legsta

Citations


Privitera GF, Cannata AA, Campanile F, Alaimo S, Bongiorno D, Pulvirenti A. BacExplorer (2024). Available at https://github.com/gretep/BacExplorer

Tools used in BacExplorer:

Package/Tool Reference
SPAdes v4.0.0 Prjibelski A. et al., 2017
TrimGalore v0.6.10 F. Krueger
mlst v2.23.0 T. Seemann
kraken2 v2.1.3 D. E. Wood, J. Lu & B. Langmead, 2019
ABRicate v1.0.1 T. Seemann
CARD v.3.3.0 Alcock et al. 2023
Megares v.2 E. Doster et al., 2019
Resfinder AF Florensa et al., 2022
ARG-ANNOT v.6 SK Gupta et al., 2014
VFDB L. Bo et al., 2022
PlasmidFinder v.2.2.0 O. Lund, 2014
ecoli_vf ecoli_vf
ecoh DJ Ingle et al., 2016
ectyper K. Bessonov et al., 2021
BLAST v2.15.0 Z. Zhang et al., 2000
AMRFinderPlus v3.12.8 M. Feldgarden et al., 2019
R v4.4.0 R Core Team, 2024
complexHeatmap v2.20.0 Gu et al., 2016
rmarkdown v2.27 Allaire et al., 2022
kableExtra v1.4.0 H. Zhu, 2024
circlize v0.4.16 Z. Gu, 2014
stringr v1.5.1 H. Wickham, 2023
dplyr v1.1.4 Wickham et al., 2023
VirulenceFinder v2.0.4 Joensen et al., 2014
Kleborate v3.1.2 Wyres KL, et al., 2021
emmtyper v0.2.0 Frost, H. R. et al., 2020
agrvate v1.0.2 V Raghuram, 2022
sccmec v1.2.0 Petit, Robert A 3rd, and Timothy D Read, 2018
spaTyper v0.3.3 MJ Sull
Legsta v0.5.1 T. Seemann
LisSero v0.4.9 Doumith M, 2004
ShigaTyper v2.0.5 Wu Y., 2019
pbptyper v2.0.0 Petit III RA
hicap v1.0.4 SC Watts
SISTR v1.1.2 C Yoshida
geNomad v.1.8.0 AP Camargo et al., 2023